normal Backward Mapping for lipid (CHOL): cannot compile

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2 years 9 months ago #8999 by Pham
Hi all!
I am currently a student and trying to learn how to use the reverse mapping tool. I tried the tutorial on aquaporin and it ran smoothly. But when apply the procedure to the lipid (I'm testing with 1 CHOL), I got in with a few troubles:

- The forcefields (ambers, charmms,...) available in my gromacs (version 467) does not have lipids itp. I found the Slipids force field which has lipids itp. Later, I found the github of Backward and got the Slipid support version, but the backward.py keeps running into error:

execute: ./initram.sh -f CHOL-cg.gro -o rcg1.gro -to slipids -p topol.top

initram.sh version 0.1:

(c)2013 Tsjerk A. Wassenaar, PhD

University of Calgary
2500 University Drive NW
Calgary, Alberta
Canada, T2N 1N4

Now executing...

./initram.sh -f CHOL-cg.gro -o rcg1.gro -to slipids -p topol.top

Checking dependencies:
backward.py ... ./backward.py
grompp_mpi ... /usr/local/gromacs467/bin/grompp_mpi
mdrun_mpi ... /usr/local/gromacs467/bin/mdrun_mpi

/backward.py -f CHOL-cg.gro -raw projected.gro -o 0-backward.gro -kick 0.05 -sol -p topol.top -po backmapped.top -n backmapped.ndx -from martini -to slipids
Traceback (most recent call last):
File "/backward.py", line 14, in <module>
import Mapping
File "/Mapping/__init__.py", line 186
print "Problem determining mapping coordinates for atom %s of residue %s."%(target[0],resn)
^
SyntaxError: invalid syntax


I twisted the script a little since I know the old backward.py I used for the tutorial worked. I replaced the new backward.py with old one, and edited the levels variable to have more ff (sorry if I did something terribly wrong, I just try to solve it....). Then, the tools somewhat compiled but with old force fields only (still fail with slipid, opls, opls-aa :(( ). At least when I set the target force field to amber99sb, the initial structure is generated (backward.py passed!), but the energy minimization cannot run.

I suspect it is because of my messy force fields (I used CHOL.itp from Slipids, but the target force field is AMBER since I heard that AMBER and Slipids can cooperate??). I am noob so I do not know what force field to use and how to use them. I tried to find sources and tutorials but no luck. I hope someone and instruct me how to convert the CG lipids to AA lipids.

So, the question is: what is wrong here? and do you have any suggestion how can I make it right? Please help me, I got stuck cluelessly for 2 days.
.......................

Here is the folder I am working on: www.dropbox.com/sh/djc82fks4wbaksp/AADjt...NnUXOwkvtXPEaua?dl=0

and here is my email: This email address is being protected from spambots. You need JavaScript enabled to view it.

I hope someone can help me with this, since I am so new to all of these tools and concepts.

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2 years 9 months ago #9005 by riccardo
Hi. The error you showed:

...
print "Problem determining mapping coordinates for atom %s of residue %s."%(target[0],resn)
^
SyntaxError: invalid syntax

seems a python 2 (expected by that version of backward.py) vs python 3 (used instead apparently to run the script). Can you make sure you run that with python 2?

However, you said you managed to run the tutorial and got backward.py to run somehow at some point so I'm confused.

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2 years 9 months ago #9006 by Pham
Sorry for confusing you. You made a great point. My PC has default python2.

I changed the version to python3. I also modified the force field I was using -
amber14sb - since it does not have lipids atomtypes declared at all (I don't know why...). Then I got the reverse mapping (new one from github) applied on a single molecule test model, and it ran perfectly. Thank you so much for your help!!!!!

(About how I modified my force field to have lipids parameters:
I extended the working force field -amber14sb- by combining the amber14sb I got from www.gromacs.org/Downloads/User_contributions/Force_fields with some of the Slipids parameters, using technique introduced in www.gromacs.org/Documentation_of_outdate...due_to_a_Force_Field )



BUT, when I use the same technique (which I used for the single molecule test, for the whole raft), I got an error like below:
./initram.sh -f 2ns-raft-e-md-DIPCtoDOPC.pdb -o CO-raft-only-aa.gro -p aa-topol.top -to amber99sb -keep

GROMACS VERSION: 4 6 7
MPI: true
/Users/pham/00-test-raft/CO-raft-only-01/backward.py -f 2ns-raft-e-md-DIPCtoDOPC.pdb -raw projected.gro -o 0-backward.gro -kick 0.05 -sol -p aa-topol.top -po backmapped.top -n backmapped.ndx -from martini -to amber99sb -solname SOL
Error reading charmm27 to martini mapping for DOPE (file: /Users/pham/00-test-raft/CO-raft-only-01/Mapping/dmpc.gromos.map).
Error reading charmm36 to martini mapping for DOPE (file: /Users/pham/00-test-raft/CO-raft-only-01/Mapping/dmpc.gromos.map).
Error reading slipids to martini mapping for DOPE (file: /Users/pham/00-test-raft/CO-raft-only-01/Mapping/dmpc.gromos.map).
Error reading amber to martini mapping for DOPE (file: /Users/pham/00-test-raft/CO-raft-only-01/Mapping/dmpc.gromos.map).
Error reading charmm27 to martini mapping for TOCL2 (file: /Users/pham/00-test-raft/CO-raft-only-01/Mapping/popc.alex.map).
Error reading charmm36 to martini mapping for TOCL2 (file: /Users/pham/00-test-raft/CO-raft-only-01/Mapping/popc.alex.map).
Error reading slipids to martini mapping for TOCL2 (file: /Users/pham/00-test-raft/CO-raft-only-01/Mapping/popc.alex.map).
Error reading amber to martini mapping for TOCL2 (file: /Users/pham/00-test-raft/CO-raft-only-01/Mapping/popc.alex.map).
Error reading charmm27 to martini mapping for DOPG (file: /Users/pham/00-test-raft/CO-raft-only-01/Mapping/dopc.gromos.map).
Error reading charmm36 to martini mapping for DOPG (file: /Users/pham/00-test-raft/CO-raft-only-01/Mapping/dopc.gromos.map).
Error reading slipids to martini mapping for DOPG (file: /Users/pham/00-test-raft/CO-raft-only-01/Mapping/dopc.gromos.map).
Error reading amber to martini mapping for DOPG (file: /Users/pham/00-test-raft/CO-raft-only-01/Mapping/dopc.gromos.map).
Error reading charmm36 to martini mapping for REYP (file: /Users/pham/00-test-raft/CO-raft-only-01/Mapping/tyr.gromos.map).
Error reading charmm27 to martini mapping for POPG (file: /Users/pham/00-test-raft/CO-raft-only-01/Mapping/heptane.gromos.map).
Error reading charmm36 to martini mapping for POPG (file: /Users/pham/00-test-raft/CO-raft-only-01/Mapping/heptane.gromos.map).
Error reading slipids to martini mapping for POPG (file: /Users/pham/00-test-raft/CO-raft-only-01/Mapping/heptane.gromos.map).
Error reading amber to martini mapping for POPG (file: /Users/pham/00-test-raft/CO-raft-only-01/Mapping/heptane.gromos.map).
Error reading charmm to martini mapping for TOG (file: /Users/pham/00-test-raft/CO-raft-only-01/Mapping/dops.charmm36.map).
Error reading charmm36 to martini mapping for TOG (file: /Users/pham/00-test-raft/CO-raft-only-01/Mapping/dops.charmm36.map).
Error reading charmm27 to martini mapping for DOPS (file: /Users/pham/00-test-raft/CO-raft-only-01/Mapping/glu.gromos.map).
Error reading charmm36 to martini mapping for DOPS (file: /Users/pham/00-test-raft/CO-raft-only-01/Mapping/glu.gromos.map).
Error reading slipids to martini mapping for DOPS (file: /Users/pham/00-test-raft/CO-raft-only-01/Mapping/glu.gromos.map).
Error reading amber to martini mapping for DOPS (file: /Users/pham/00-test-raft/CO-raft-only-01/Mapping/glu.gromos.map).
Residues defined for transformation from martini to amber99sb:
dict_keys()
None
Not all positions defined for [out] in residue CHO:
C2 dict_keys()
Traceback (most recent call last):
File "/Users/pham/00-test-raft/CO-raft-only-01/backward.py", line 959, in <module>
o, r = mapping[resn].do(residue,target,bb,nterm,cterm,options["-nt"])
File "/Users/pham/00-test-raft/CO-raft-only-01/Mapping/__init__.py", line 489, in do
out[t] = out[t][:4] + coord[i[0]]
TypeError: can only concatenate tuple (not "NoneType") to tuple


My topology looks like below, with CHOL, DPPC, and DOPC itp files downloaded from Slipids www.fos.su.se/~sasha/SLipids/Downloads.html

; Include forcefield parameters
#include "amber14sb-lipids.ff/forcefield.itp"

; Include lipids itp
#include "CHOL.itp"
#include "DPPC.itp"
#include "DOPC.itp"

; Include chain topologies
#include "martini_v2.0_lipids_all_201506.itp"

; Include water topology
; #include "amber14sb-lipids.ff/tip3p.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif

[ system ]
; Name
Backmapped structure from MARTINI to amber99sb for CO raft

[ molecules ]
; name number
CHOL 576
DPPC 828
DOPC 540


The full design folder can be found here: drive.google.com/drive/folders/1kmxTSp3y...0D5WHe31?usp=sharing

What part did I do wrong?

Thank you again to be patient with me. I appreciate your help a lot.

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2 years 9 months ago #9012 by riccardo
Mmh, can't tell just from this. So, that's what I'd do (since for 1 test molecule everything works): try to backmap systems with increased complexity with the molecules you need, that is:

1) system with only 1 CHOL molecule
2) system with 1 CHOL and 1 DPPC molecules
3) system with 1 CHOL, 1 DPPC, and 1 DOPC

Can you try this? Let's see then which steps you can get done and at which step you get stuck.
I would just use the actual "2ns-raft-e-md-DIPCtoDOPC.pdb" and just delete all but 1 molecule for test 1), all but those 2 molecules for step 2), etc.

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2 years 9 months ago #9014 by Pham
I found a way to work around that! When I tested it with a different raft, it ran quite fine. I think the difference is that:
- For the failed one: I manually removed all the solvents from the designed raft and might have made some mistakes there.
- For the succeeded one: I used the PDB raft that has already run through MD simulation (not just a raw design). I also used the Gromacs tools such as editconf, trjconv, make_ndx... to automatically extracted the PDB without water. This way is safer (I got suggested) since those tools may have the checking for generated outputs.

I was able to have everything converted (at least to the EM steps, I still need to design position restraint things...).
Now, I'm looking for the GM1 (DBG in coarse-grained) atomistic itp to build another topology for another raft. I saw the mapping is available, and saw Dr. Tieleman's research on that CG & AA GM1, but couldn't find the atomistic structure file anywhere online. If you by chance have the .itp/.top, or know where I can find it, please help! (can email me at This email address is being protected from spambots. You need JavaScript enabled to view it.)
One minor error I detected from the backward.py script is about the mpi run. As I understand, in backward.py (line 361-370), the logic was off, making the MPI run not executed. I think we just need to simply swap the logic to fix it. I did and got my EM runs noticeably faster when execute on 4 threads. Hope this helps!

# Set up for running
G="$GROMPP -f $mdp -c $GRO -n $NDX -p $OTP -o $BASE -maxwarn 2"
echo $G; $G || exit

if $MPI
then
NT=
else
NT="-nt $EMNP"
fi


Overall, I learned a lot from the last few days, and your support helped me so much in learning how to use the tools. Thank you for helping out a newbie like me! :))) Have a wonderful day!

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2 years 9 months ago #9017 by riccardo
Great! Happy to hear.

Regarding the GM1 AA itp, I don't have that/know where it is. I would recommend to check the associated publications and if you don't find it still, contact the corresponding authors of those.

Regarding the MPI backward issue, I think it would be best if you opened an issue on the Github page of backward to better keep track of the issue and get someone to have a look at it: github.com/Tsjerk/Backward/issues

have a great day you too!

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2 years 9 months ago #9024 by hind
Hi,
I get the same error, could you please help me to fix it.
Not all positions defined for [chiral] in residue CHOL;
H25 ...

Thanks

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2 years 9 months ago #9025 by Pham
May you post the full error (and maybe a few lines of topol, coordinate files...)? I might have met the error and help if I see more information. :)

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2 years 9 months ago #9026 by hind
./backward.py -f 1pdb_em.gro -raw projected.gro -o 0-backward.gro -kick 0.05 -sol -p topol.top -po backmapped.top -n backmapped.ndx -from martini -to charmm36 -mapdir ./Mapping/
Error reading charmm to martini mapping for TOG (file: ./Mapping/PC44.alex.map).
Error reading charmm36 to martini mapping for TOG (file: ./Mapping/PC44.alex.map).
Error reading charmm27 to martini mapping for DOPS (file: ./Mapping/dopc.gromos.map).
Error reading charmm36 to martini mapping for DOPS (file: ./Mapping/dopc.gromos.map).
Error reading slipids to martini mapping for DOPS (file: ./Mapping/dopc.gromos.map).
Error reading amber to martini mapping for DOPS (file: ./Mapping/dopc.gromos.map).
Error reading charmm27 to martini mapping for POPG (file: ./Mapping/cys.gromos.map).
Error reading charmm36 to martini mapping for POPG (file: ./Mapping/cys.gromos.map).
Error reading slipids to martini mapping for POPG (file: ./Mapping/cys.gromos.map).
Error reading amber to martini mapping for POPG (file: ./Mapping/cys.gromos.map).
Error reading charmm27 to martini mapping for DOPG (file: ./Mapping/tyr.charmm36.map).
Error reading charmm36 to martini mapping for DOPG (file: ./Mapping/tyr.charmm36.map).
Error reading slipids to martini mapping for DOPG (file: ./Mapping/tyr.charmm36.map).
Error reading amber to martini mapping for DOPG (file: ./Mapping/tyr.charmm36.map).
Error reading charmm27 to martini mapping for DOPE (file: ./Mapping/leu.amber.map).
Error reading charmm36 to martini mapping for DOPE (file: ./Mapping/leu.amber.map).
Error reading slipids to martini mapping for DOPE (file: ./Mapping/leu.amber.map).
Error reading amber to martini mapping for DOPE (file: ./Mapping/leu.amber.map).
Error reading charmm36 to martini mapping for REYP (file: ./Mapping/phe.amber.map).
Error reading charmm27 to martini mapping for TOCL2 (file: ./Mapping/chl1.charmm36.map).
Error reading charmm36 to martini mapping for TOCL2 (file: ./Mapping/chl1.charmm36.map).
Error reading slipids to martini mapping for TOCL2 (file: ./Mapping/chl1.charmm36.map).
Error reading amber to martini mapping for TOCL2 (file: ./Mapping/chl1.charmm36.map).
Residues defined for transformation from martini to charmm36:
dict_keys()
None
Not all positions defined for [chiral] in residue CHL1:
H25 dict_keys()
Traceback (most recent call last):
File "./backward.py", line 959, in <module>
o, r = mapping[resn].do(residue,target,bb,nterm,cterm,options["-nt"])
File "/home/siddiqh/Desktop/luna/APOA1_10system/Backward-master/aa_copy/Mapping/__init__.py", line 489, in do
out[t] = out[t][:4] + coord[i[0]]
TypeError: can only concatenate tuple (not "NoneType") to tuple

###############
all atom topol.top

; Include forcefield parameters
#include "./charmm36-jul2020.ff/forcefield.itp"

; Include chain topologies
#include "topol_Protein_chain_A.itp"
#include "topol_Protein_chain_B.itp"
#include "topol_Other_chain_M.itp"

; Include water topology
#include "TIP3.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif

; Include topology for ions
#include "ions.itp"

[ system ]
; Name
Gromacs Runs One Microsecond At Cannonball Speeds

[ molecules ]
; Compound #mols
Protein_chain_A 1
Protein_chain_B 1
Other_chain_M 1
;TIP3 95199
;NA 1136
;CL 1118

####################
## this all atom itp of one cholesterol ##
; residue 687 CHL1 rtp CHL1 q 0.0
26801 CRL1 687 CHL1 C3 26801 0.14 12.011 ; qtot 0.14
26802 HGA1 687 CHL1 H3 26802 0.09 1.008 ; qtot 0.23
26803 OHL 687 CHL1 O3 26803 -0.66 15.9994 ; qtot -0.43
26804 HOL 687 CHL1 H3' 26804 0.43 1.008 ; qtot 0
26805 CRL2 687 CHL1 C4 26805 -0.18 12.011 ; qtot -0.18
26806 HGA2 687 CHL1 H4A 26806 0.09 1.008 ; qtot -0.09
26807 HGA2 687 CHL1 H4B 26807 0.09 1.008 ; qtot 0
26808 CEL1 687 CHL1 C5 26808 0 12.011 ; qtot 0
26809 CEL1 687 CHL1 C6 26809 -0.15 12.011 ; qtot -0.15
26810 HEL1 687 CHL1 H6 26810 0.15 1.008 ; qtot 0
26811 CRL2 687 CHL1 C7 26811 -0.18 12.011 ; qtot -0.18
26812 HGA2 687 CHL1 H7A 26812 0.09 1.008 ; qtot -0.09
26813 HGA2 687 CHL1 H7B 26813 0.09 1.008 ; qtot 0
26814 CRL1 687 CHL1 C8 26814 -0.09 12.011 ; qtot -0.09
26815 HGA1 687 CHL1 H8 26815 0.09 1.008 ; qtot 0
26816 CRL1 687 CHL1 C14 26816 -0.09 12.011 ; qtot -0.09
26817 HGA1 687 CHL1 H14 26817 0.09 1.008 ; qtot 0
26818 CRL2 687 CHL1 C15 26818 -0.18 12.011 ; qtot -0.18
26819 HGA2 687 CHL1 H15A 26819 0.09 1.008 ; qtot -0.09
26820 HGA2 687 CHL1 H15B 26820 0.09 1.008 ; qtot 0
26821 CRL2 687 CHL1 C16 26821 -0.18 12.011 ; qtot -0.18
26822 HGA2 687 CHL1 H16A 26822 0.09 1.008 ; qtot -0.09
26823 HGA2 687 CHL1 H16B 26823 0.09 1.008 ; qtot 0
26824 CRL1 687 CHL1 C17 26824 -0.09 12.011 ; qtot -0.09
26825 HGA1 687 CHL1 H17 26825 0.09 1.008 ; qtot 0
26826 CRL1 687 CHL1 C13 26826 0 12.011 ; qtot 0
26827 CTL3 687 CHL1 C18 26827 -0.27 12.011 ; qtot -0.27
26828 HAL3 687 CHL1 H18A 26828 0.09 1.008 ; qtot -0.18
26829 HAL3 687 CHL1 H18B 26829 0.09 1.008 ; qtot -0.09
26830 HAL3 687 CHL1 H18C 26830 0.09 1.008 ; qtot 0
26831 CRL2 687 CHL1 C12 26831 -0.18 12.011 ; qtot -0.18
26832 HGA2 687 CHL1 H12A 26832 0.09 1.008 ; qtot -0.09
26833 HGA2 687 CHL1 H12B 26833 0.09 1.008 ; qtot 0
26834 CRL2 687 CHL1 C11 26834 -0.18 12.011 ; qtot -0.18
26835 HGA2 687 CHL1 H11A 26835 0.09 1.008 ; qtot -0.09
26836 HGA2 687 CHL1 H11B 26836 0.09 1.008 ; qtot 0
26837 CRL1 687 CHL1 C9 26837 -0.09 12.011 ; qtot -0.09
26838 HGA1 687 CHL1 H9 26838 0.09 1.008 ; qtot 0
26839 CRL1 687 CHL1 C10 26839 0 12.011 ; qtot 0
26840 CTL3 687 CHL1 C19 26840 -0.27 12.011 ; qtot -0.27
26841 HAL3 687 CHL1 H19A 26841 0.09 1.008 ; qtot -0.18
26842 HAL3 687 CHL1 H19B 26842 0.09 1.008 ; qtot -0.09
26843 HAL3 687 CHL1 H19C 26843 0.09 1.008 ; qtot 0
26844 CRL2 687 CHL1 C1 26844 -0.18 12.011 ; qtot -0.18
26845 HGA2 687 CHL1 H1A 26845 0.09 1.008 ; qtot -0.09
26846 HGA2 687 CHL1 H1B 26846 0.09 1.008 ; qtot 0
26847 CRL2 687 CHL1 C2 26847 -0.18 12.011 ; qtot -0.18
26848 HGA2 687 CHL1 H2A 26848 0.09 1.008 ; qtot -0.09
26849 HGA2 687 CHL1 H2B 26849 0.09 1.008 ; qtot 0
26850 CTL1 687 CHL1 C20 26850 -0.09 12.011 ; qtot -0.09
26851 HAL1 687 CHL1 H20 26851 0.09 1.008 ; qtot 0
26852 CTL3 687 CHL1 C21 26852 -0.27 12.011 ; qtot -0.27
26853 HAL3 687 CHL1 H21A 26853 0.09 1.008 ; qtot -0.18
26854 HAL3 687 CHL1 H21B 26854 0.09 1.008 ; qtot -0.09
26855 HAL3 687 CHL1 H21C 26855 0.09 1.008 ; qtot 0
26856 CTL2 687 CHL1 C22 26856 -0.18 12.011 ; qtot -0.18
26857 HAL2 687 CHL1 H22A 26857 0.09 1.008 ; qtot -0.09
26858 HAL2 687 CHL1 H22B 26858 0.09 1.008 ; qtot 0
26859 CTL2 687 CHL1 C23 26859 -0.18 12.011 ; qtot -0.18
26860 HAL2 687 CHL1 H23A 26860 0.09 1.008 ; qtot -0.09
26861 HAL2 687 CHL1 H23B 26861 0.09 1.008 ; qtot 0
26862 CTL2 687 CHL1 C24 26862 -0.18 12.011 ; qtot -0.18
26863 HAL2 687 CHL1 H24A 26863 0.09 1.008 ; qtot -0.09
26864 HAL2 687 CHL1 H24B 26864 0.09 1.008 ; qtot 0
26865 CTL1 687 CHL1 C25 26865 -0.09 12.011 ; qtot -0.09
26866 HAL1 687 CHL1 H25 26866 0.09 1.008 ; qtot 0
26867 CTL3 687 CHL1 C26 26867 -0.27 12.011 ; qtot -0.27
26868 HAL3 687 CHL1 H26A 26868 0.09 1.008 ; qtot -0.18
26869 HAL3 687 CHL1 H26B 26869 0.09 1.008 ; qtot -0.09
26870 HAL3 687 CHL1 H26C 26870 0.09 1.008 ; qtot 0
26871 CTL3 687 CHL1 C27 26871 -0.27 12.011 ; qtot -0.27
26872 HAL3 687 CHL1 H27A 26872 0.09 1.008 ; qtot -0.18
26873 HAL3 687 CHL1 H27B 26873 0.09 1.008 ; qtot -0.09
26874 HAL3 687 CHL1 H27C 26874 0.09 1.008 ; qtot 0

cg.gro of one cholesterol
444CHL1 ROH 3485 22.567 18.782 5.149
444CHL1 R1 3486 22.535 19.055 5.214
444CHL1 R2 3487 22.409 19.234 5.047
444CHL1 R3 3488 22.258 19.284 5.267
444CHL1 R4 3489 22.222 19.521 5.099
444CHL1 R5 3490 22.285 19.519 5.307
444CHL1 C1 3491 21.971 19.734 5.336
444CHL1 C2 3492 21.697 19.979 5.521

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2 years 9 months ago #9027 by Pham
I personally only use the wrapper initram.sh, thus not have much experience with the backward.py.
But looking at your files, I can say that the error is most likely because your cg.gro is formatted wrong.

To feed the gro file to backward script, the format is important for the script to see the content. Meaning each space in .gro matters.

If you can, I suggest you feeding the script with .pdb file, which has much better format consistency.

Otherwise, if you still want to use gro, my format for CHOL cg .gro is in the drive link here:
( only trust the gro and topol files, other files might already modified by me :))

drive.google.com/drive/folders/1gYDZZqHa...dUBACbrW?usp=sharing

I always use initram.sh wrapper :), and what I executed is (for 1 CHOL molecule system):

./initram.sh -f CHOL-cg.gro -p topol.top -o aa.gro -to amber99sb

Try it and see wether or not it solve the problem.
Hope this help!!

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2 years 9 months ago #9028 by hind
thanks for your kind

i use ./initram.sh with pdb format and i still get the error

pdb
ATOM 3485 ROH CHL1 444 225.670 187.820 51.490 1.00 0.00
ATOM 3486 R1 CHL1 444 225.350 190.550 52.140 1.00 0.00
ATOM 3487 R2 CHL1 444 224.090 192.340 50.470 1.00 0.00
ATOM 3488 R3 CHL1 444 222.580 192.840 52.670 1.00 0.00
ATOM 3489 R4 CHL1 444 222.220 195.210 50.990 1.00 0.00
ATOM 3490 R5 CHL1 444 222.850 195.190 53.070 1.00 0.00
ATOM 3491 C1 CHL1 444 219.710 197.340 53.360 1.00 0.00
ATOM 3492 C2 CHL1 444 216.970 199.790 55.210 1.00 0.00
######################
topol.top
; Include forcefield parameters
#include "charmm36-jul2020.ff/forcefield.itp"
#include "PROA.itp"
#include "POPC.itp"
#include "CHL1.itp"


[ system ]
; Name
Title

[ molecules ]
; Compound #mols
PROA 2
POPC 200
CHL1 20

#################
./initram.sh -f 1pdb_em.pdb -p topol.top -to charmm36 -o aa.gro

initram.sh version 0.1:

(c)2014 Tsjerk A. Wassenaar, PhD

Computational Biology
Friedrich-Alexander University Erlangen-Nuernberg
Staudstrasse 5
91058 Erlangen
Germany


Now executing...

./initram.sh -f 1pdb_em.pdb -p topol.top -to charmm36 -o aa.gro

GROMACS VERSION: 2018 2
MPI: false
/home/siddiqh/Desktop/luna/APOA1_10system/Backward-master/aa_copy/backward.py -f 1pdb_em.pdb -raw projected.gro -o 0-backward.gro -kick 0.05 -sol -p topol.top -po backmapped.top -n backmapped.ndx -from martini -to charmm36 -solname SOL
Error reading charmm to martini mapping for TOG (file: /home/siddiqh/Desktop/luna/APOA1_10system/Backward-master/aa_copy/Mapping/PC44.alex.map).
Error reading charmm36 to martini mapping for TOG (file: /home/siddiqh/Desktop/luna/APOA1_10system/Backward-master/aa_copy/Mapping/PC44.alex.map).
Error reading charmm27 to martini mapping for DOPS (file: /home/siddiqh/Desktop/luna/APOA1_10system/Backward-master/aa_copy/Mapping/dopc.gromos.map).
Error reading charmm36 to martini mapping for DOPS (file: /home/siddiqh/Desktop/luna/APOA1_10system/Backward-master/aa_copy/Mapping/dopc.gromos.map).
Error reading slipids to martini mapping for DOPS (file: /home/siddiqh/Desktop/luna/APOA1_10system/Backward-master/aa_copy/Mapping/dopc.gromos.map).
Error reading amber to martini mapping for DOPS (file: /home/siddiqh/Desktop/luna/APOA1_10system/Backward-master/aa_copy/Mapping/dopc.gromos.map).
Error reading charmm27 to martini mapping for POPG (file: /home/siddiqh/Desktop/luna/APOA1_10system/Backward-master/aa_copy/Mapping/cys.gromos.map).
Error reading charmm36 to martini mapping for POPG (file: /home/siddiqh/Desktop/luna/APOA1_10system/Backward-master/aa_copy/Mapping/cys.gromos.map).
Error reading slipids to martini mapping for POPG (file: /home/siddiqh/Desktop/luna/APOA1_10system/Backward-master/aa_copy/Mapping/cys.gromos.map).
Error reading amber to martini mapping for POPG (file: /home/siddiqh/Desktop/luna/APOA1_10system/Backward-master/aa_copy/Mapping/cys.gromos.map).
Error reading charmm27 to martini mapping for DOPG (file: /home/siddiqh/Desktop/luna/APOA1_10system/Backward-master/aa_copy/Mapping/tyr.charmm36.map).
Error reading charmm36 to martini mapping for DOPG (file: /home/siddiqh/Desktop/luna/APOA1_10system/Backward-master/aa_copy/Mapping/tyr.charmm36.map).
Error reading slipids to martini mapping for DOPG (file: /home/siddiqh/Desktop/luna/APOA1_10system/Backward-master/aa_copy/Mapping/tyr.charmm36.map).
Error reading amber to martini mapping for DOPG (file: /home/siddiqh/Desktop/luna/APOA1_10system/Backward-master/aa_copy/Mapping/tyr.charmm36.map).
Error reading charmm27 to martini mapping for DOPE (file: /home/siddiqh/Desktop/luna/APOA1_10system/Backward-master/aa_copy/Mapping/leu.amber.map).
Error reading charmm36 to martini mapping for DOPE (file: /home/siddiqh/Desktop/luna/APOA1_10system/Backward-master/aa_copy/Mapping/leu.amber.map).
Error reading slipids to martini mapping for DOPE (file: /home/siddiqh/Desktop/luna/APOA1_10system/Backward-master/aa_copy/Mapping/leu.amber.map).
Error reading amber to martini mapping for DOPE (file: /home/siddiqh/Desktop/luna/APOA1_10system/Backward-master/aa_copy/Mapping/leu.amber.map).
Error reading charmm36 to martini mapping for REYP (file: /home/siddiqh/Desktop/luna/APOA1_10system/Backward-master/aa_copy/Mapping/phe.amber.map).
Error reading charmm27 to martini mapping for TOCL2 (file: /home/siddiqh/Desktop/luna/APOA1_10system/Backward-master/aa_copy/Mapping/chl1.charmm36.map).
Error reading charmm36 to martini mapping for TOCL2 (file: /home/siddiqh/Desktop/luna/APOA1_10system/Backward-master/aa_copy/Mapping/chl1.charmm36.map).
Error reading slipids to martini mapping for TOCL2 (file: /home/siddiqh/Desktop/luna/APOA1_10system/Backward-master/aa_copy/Mapping/chl1.charmm36.map).
Error reading amber to martini mapping for TOCL2 (file: /home/siddiqh/Desktop/luna/APOA1_10system/Backward-master/aa_copy/Mapping/chl1.charmm36.map).
Residues defined for transformation from martini to charmm36:
dict_keys()
None
Not all positions defined for [chiral] in residue CHL1:
H25 dict_keys()
Traceback (most recent call last):
File "/home/siddiqh/Desktop/luna/APOA1_10system/Backward-master/aa_copy/backward.py", line 959, in <module>
o, r = mapping[resn].do(residue,target,bb,nterm,cterm,options["-nt"])
File "/home/siddiqh/Desktop/luna/APOA1_10system/Backward-master/aa_copy/Mapping/__init__.py", line 489, in do
out[t] = out[t][:4] + coord[i[0]]
TypeError: can only concatenate tuple (not "NoneType") to tuple

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  • Pham
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2 years 9 months ago #9029 by Pham
can it be because of the naming? in Mapping, they search for the molecule name CHOL, not CHL1 tho.

ex: in chol.charmm36.map

[ molecule ]
CHOL

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  • hind
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2 years 9 months ago #9030 by hind
i use it chl1.charmm36.map

[ molecule ]
CHL1

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2 years 9 months ago #9031 by Pham
Did you change it yourself? the default Mapping does not have chl1.*.map tho

Most recent version can be found here:
github.com/Tsjerk/Backward

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  • hind
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2 years 9 months ago #9032 by hind
because in charmm36-jul2020.ff/forcefield.itp the name is CHLI, so i copy chol.charmm36.map and i change the name

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2 years 9 months ago #9033 by Pham
can you send me the coordinate file and the topology (+itp)? (This email address is being protected from spambots. You need JavaScript enabled to view it.) I can try it out. And you use the charmm36 from mackerell.umaryland.edu/charmm_ff.shtml#gromacs ?

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2 years 9 months ago #9034 by hind
sorry i ment the name in r2p of charmm named chl1, so when i built the system i keep the same name.
i will change the name to chol and see if its work

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2 years 9 months ago #9035 by hind
i changed the name to CHOL in topol.top and pdb , it still the same error.
anyone have an idea how to solve this error, I would be grateful

Thanks

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2 years 9 months ago #9036 by hind
i will send it
yes i used charmm36 from that web page
Thanks

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2 years 9 months ago #9037 by Pham
I tried to regenerate the error I made. And I found that I made a mistake in the topology. One of my #include is the martini FF, which is a CG FF.

; Include chain topologies
#include "martini_v2.0_lipids_all_201506.itp"

I don't really need it. So removing that line help my model overcame the "TypeError: can only concatenate tuple (not "NoneType") to tuple".

Try checking all of the #include in your topology and making sure that all of them are parameters of your target FF (charmm36?) or compatible with it. In otherword, checking
+ coordinate file matches right column of .map file? topol's itp matches left column of .map files?
+ topol's molecules order matches coord file's order?

You can still send it to me and I'll help my best to check them.

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