backmap problem: New molecule (ligand) (Updated)
- albumns
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6 years 10 months ago #7286
by albumns
backmap problem: New molecule (ligand) (Updated) was created by albumns
Hello,
I would like to reverse CG results to all atom with command line:
but it always failed with messages:
My input .gro is good and I can visualize in VMD... I am just wondering how to solve this problem?
Thx a lot
I would like to reverse CG results to all atom with command line:
./initram.sh -f comp1x.gro -o aa_charmm.gro -to charmm36 -p topol.topbut it always failed with messages:
-------------------------------------------------------
Program grompp, VERSION 4.5.7
Source code file: grompp.c, line: 523
Fatal error:
number of coordinates in coordinate file (0-backward.gro, 0)
does not match topology (backmapped.top, 1387)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
"Shit Happens" (Pulp Fiction)My input .gro is good and I can visualize in VMD... I am just wondering how to solve this problem?
Thx a lot
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- riccardo
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6 years 10 months ago #7288
by riccardo
Replied by riccardo on topic backmap problem: New molecule (ligand) (Updated)
Looks like nothing gets projected.
You're missing a flag (-from martini, see for example cgmartini.nl/index.php/component/kunena/...-mapping-mthods#7284 ) in your initram command but I suppose "martini" may just be the default so probably not needed (but you could still try it).
Another thing I would do is try to backmap a minimal example, as just one molecule of your system in vacuum. Have you tried that?
You're missing a flag (-from martini, see for example cgmartini.nl/index.php/component/kunena/...-mapping-mthods#7284 ) in your initram command but I suppose "martini" may just be the default so probably not needed (but you could still try it).
Another thing I would do is try to backmap a minimal example, as just one molecule of your system in vacuum. Have you tried that?
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4 years 2 weeks ago - 4 years 2 weeks ago #8480
by bhupendra123
Replied by bhupendra123 on topic backmap problem: New molecule (ligand) (Updated)
I have a simple question.
Can I use this backmapping protocol for a new molecule such as ligand?
If yes; then how?
I need some help.
I am trying to use this back mapping protocol for another new molecule (my CG Ligand molecule).
My ligand is a simple 3-bead CG benzene molecule that I want to convert back to the atomistic benzene molecule.
In the paper, it is said that this script can be used for the conversion of any molecule from MARTINI to Atomistic and vice versa, provided the mapping can be written.
I am attaching my ligand gro file, mapping file, and the topology file along with a separate post.
I have also included my ligand (so-called residue name "BENZ") in the backward.py file and __init__.py file.
Do I need to create a special entry list for these other types of molecules as we have for amino acids, lipids, nucleic acids?
I want to know what are the necessary changes required to make in the script ( backward.py, __init__.py and also in the initram-v5.sh) file so that we can use it for another new molecule.
I followed the instruction and built the reverse mapping file for my ligand by making required changes in all the script files. But I am getting the following error:
###############################################
Fatal error:
number of coordinates in coordinate file (0-backward.gro, 0)
does not match topology (backmapped.top, 8824)
################################################
I just want to test the script for the given mapping. Later I will improve the mapping accordingly.
I think my system is getting blown up that is why it has 0 atoms or maybe because of some other reasons. I want to understand why it is happening and where I am making a mistake. I eagerly want to learn this reverse mapping. I have already learned the MARTINI coarse-grain method and I need to use this back mapping technique in my research work.
I want to try this protocol for this simple ligand first. Then I will try it for other complicated ligands.
I request you to please give me some help or advice or suggestions regarding this problem.
Any help will be appreciated.
Thank you so much
###############command I used:####################
./initram-v5.sh -f benz.gro -o benz_charmm.gro -from martini -to charmm36 -p topol.top
Can I use this backmapping protocol for a new molecule such as ligand?
If yes; then how?
I need some help.
I am trying to use this back mapping protocol for another new molecule (my CG Ligand molecule).
My ligand is a simple 3-bead CG benzene molecule that I want to convert back to the atomistic benzene molecule.
In the paper, it is said that this script can be used for the conversion of any molecule from MARTINI to Atomistic and vice versa, provided the mapping can be written.
I am attaching my ligand gro file, mapping file, and the topology file along with a separate post.
I have also included my ligand (so-called residue name "BENZ") in the backward.py file and __init__.py file.
Do I need to create a special entry list for these other types of molecules as we have for amino acids, lipids, nucleic acids?
I want to know what are the necessary changes required to make in the script ( backward.py, __init__.py and also in the initram-v5.sh) file so that we can use it for another new molecule.
I followed the instruction and built the reverse mapping file for my ligand by making required changes in all the script files. But I am getting the following error:
###############################################
Fatal error:
number of coordinates in coordinate file (0-backward.gro, 0)
does not match topology (backmapped.top, 8824)
################################################
I just want to test the script for the given mapping. Later I will improve the mapping accordingly.
I think my system is getting blown up that is why it has 0 atoms or maybe because of some other reasons. I want to understand why it is happening and where I am making a mistake. I eagerly want to learn this reverse mapping. I have already learned the MARTINI coarse-grain method and I need to use this back mapping technique in my research work.
I want to try this protocol for this simple ligand first. Then I will try it for other complicated ligands.
I request you to please give me some help or advice or suggestions regarding this problem.
Any help will be appreciated.
Thank you so much
###############command I used:####################
./initram-v5.sh -f benz.gro -o benz_charmm.gro -from martini -to charmm36 -p topol.top
Last edit: 4 years 2 weeks ago by bhupendra123. Reason: Asked to refine the post
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- riccardo
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4 years 2 weeks ago - 4 years 2 weeks ago #8481
by riccardo
Replied by riccardo on topic backmap problem: New molecule (ligand) (Updated)
Can you somehow make your post a little tidier?
Maybe link files externally or at least format the files and your text differently so that we can go through your post more easily.
You can just *edit* your post, instead of creating a new one. Just perhaps post again something like "updated" so we get notified. Thanks!
Maybe link files externally or at least format the files and your text differently so that we can go through your post more easily.
You can just *edit* your post, instead of creating a new one. Just perhaps post again something like "updated" so we get notified. Thanks!
Last edit: 4 years 2 weeks ago by riccardo.
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4 years 2 weeks ago #8482
by bhupendra123
Replied by bhupendra123 on topic backmap problem: New molecule (ligand) (Updated)
################GRO.FILE############
benzene
3
1BENZ SC5 1 1.383 1.453 1.515
1BENZ SC5 2 1.520 1.625 1.515
1BENZ SC5 3 1.597 1.424 1.470
3.00000 3.00000 3.00000
#######################################
#############BENZ.CHARMM.MAP.file#######
[ molecule ]
BENZ
[ martini ]
SC5 SC5 SC5
[ mapping ]
charmm36
[ atoms ]
1 CG2R61 SC5
2 CG2R61 SC5 SC5
3 HGR61 SC5
4 HGR61 SC5
5 CG2R61 SC5
6 CG2R61 SC5 SC5
7 HGR61 SC5
8 HGR61 SC5
9 CG2R61 SC5
10 CG2R61 SC5 SC5
11 HGR61 SC5
12 HGR61 SC5
##############################
benzene
3
1BENZ SC5 1 1.383 1.453 1.515
1BENZ SC5 2 1.520 1.625 1.515
1BENZ SC5 3 1.597 1.424 1.470
3.00000 3.00000 3.00000
#######################################
#############BENZ.CHARMM.MAP.file#######
[ molecule ]
BENZ
[ martini ]
SC5 SC5 SC5
[ mapping ]
charmm36
[ atoms ]
1 CG2R61 SC5
2 CG2R61 SC5 SC5
3 HGR61 SC5
4 HGR61 SC5
5 CG2R61 SC5
6 CG2R61 SC5 SC5
7 HGR61 SC5
8 HGR61 SC5
9 CG2R61 SC5
10 CG2R61 SC5 SC5
11 HGR61 SC5
12 HGR61 SC5
##############################
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4 years 2 weeks ago #8483
by bhupendra123
Replied by bhupendra123 on topic backmap problem: New molecule (ligand) (Updated)
####################TOPOL.TOP################
;;
;; Generated by CHARMM-GUI ( www.charmm-gui.org ) v1.7
;;
;; psf2itp.py
;;
;; Correspondance:
;; This email address is being protected from spambots. You need JavaScript enabled to view it. or This email address is being protected from spambots. You need JavaScript enabled to view it.
;;
;; GROMACS topology file for HETF
;;
[ moleculetype ]
; name nrexcl
BENZ 3
[ atoms ]
; nr type resnr residu atom cgnr charge mass
1 CG2R61 900 BNZ C3 1 -0.115 12.0110 ; qtot -0.115
2 CG2R61 900 BNZ C2 2 -0.115 12.0110 ; qtot -0.230
3 HGR61 900 BNZ H3 3 0.115 1.0080 ; qtot -0.115
4 HGR61 900 BNZ H2 4 0.115 1.0080 ; qtot 0.000
5 CG2R61 900 BNZ C1 5 -0.115 12.0110 ; qtot -0.115
6 CG2R61 900 BNZ C6 6 -0.115 12.0110 ; qtot -0.230
7 HGR61 900 BNZ H1 7 0.115 1.0080 ; qtot -0.115
8 HGR61 900 BNZ H6 8 0.115 1.0080 ; qtot 0.000
9 CG2R61 900 BNZ C5 9 -0.115 12.0110 ; qtot -0.115
10 CG2R61 900 BNZ C4 10 -0.115 12.0110 ; qtot -0.230
11 HGR61 900 BNZ H5 11 0.115 1.0080 ; qtot -0.115
12 HGR61 900 BNZ H4 12 0.115 1.0080 ; qtot 0.000
[ bonds ]
......
.....
####################################
;;
;; Generated by CHARMM-GUI ( www.charmm-gui.org ) v1.7
;;
;; psf2itp.py
;;
;; Correspondance:
;; This email address is being protected from spambots. You need JavaScript enabled to view it. or This email address is being protected from spambots. You need JavaScript enabled to view it.
;;
;; GROMACS topology file for HETF
;;
[ moleculetype ]
; name nrexcl
BENZ 3
[ atoms ]
; nr type resnr residu atom cgnr charge mass
1 CG2R61 900 BNZ C3 1 -0.115 12.0110 ; qtot -0.115
2 CG2R61 900 BNZ C2 2 -0.115 12.0110 ; qtot -0.230
3 HGR61 900 BNZ H3 3 0.115 1.0080 ; qtot -0.115
4 HGR61 900 BNZ H2 4 0.115 1.0080 ; qtot 0.000
5 CG2R61 900 BNZ C1 5 -0.115 12.0110 ; qtot -0.115
6 CG2R61 900 BNZ C6 6 -0.115 12.0110 ; qtot -0.230
7 HGR61 900 BNZ H1 7 0.115 1.0080 ; qtot -0.115
8 HGR61 900 BNZ H6 8 0.115 1.0080 ; qtot 0.000
9 CG2R61 900 BNZ C5 9 -0.115 12.0110 ; qtot -0.115
10 CG2R61 900 BNZ C4 10 -0.115 12.0110 ; qtot -0.230
11 HGR61 900 BNZ H5 11 0.115 1.0080 ; qtot -0.115
12 HGR61 900 BNZ H4 12 0.115 1.0080 ; qtot 0.000
[ bonds ]
......
.....
####################################
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4 years 2 weeks ago #8484
by bhupendra123
Replied by bhupendra123 on topic backmap problem: New molecule (ligand) (Updated)
bhupendra123 wrote: I have a simple question.
Can I use this backmapping protocol for a new molecule such as ligand?
If yes; then how?
I need some help.
I am trying to use this back mapping protocol for another new molecule (my CG Ligand molecule).
My ligand is a simple 3-bead CG benzene molecule that I want to convert back to the atomistic benzene molecule.
In the paper, it is said that this script can be used for the conversion of any molecule from MARTINI to Atomistic and vice versa, provided the mapping can be written.
I am attaching my ligand gro file, mapping file, and the topology file along with a separate post.
I have also included my ligand (so-called residue name "BENZ") in the backward.py file and __init__.py file.
Do I need to create a special entry list for these other types of molecules as we have for amino acids, lipids, nucleic acids?
I want to know what are the necessary changes required to make in the script ( backward.py, __init__.py and also in the initram-v5.sh) file so that we can use it for another new molecule.
I followed the instruction and built the reverse mapping file for my ligand by making required changes in all the script files. But I am getting the following error:
###############################################
Fatal error:
number of coordinates in coordinate file (0-backward.gro, 0)
does not match topology (backmapped.top, 8824)
################################################
I just want to test the script for the given mapping. Later I will improve the mapping accordingly.
I think my system is getting blown up that is why it has 0 atoms or maybe because of some other reasons. I want to understand why it is happening and where I am making a mistake. I eagerly want to learn this reverse mapping. I have already learned the MARTINI coarse-grain method and I need to use this back mapping technique in my research work.
I want to try this protocol for this simple ligand first. Then I will try it for other complicated ligands.
I request you to please give me some help or advice or suggestions regarding this problem.
Any help will be appreciated.
Thank you so much
###############command I used:####################
./initram-v5.sh -f benz.gro -o benz_charmm.gro -from martini -to charmm36 -p topol.top
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4 years 1 week ago #8489
by riccardo
Replied by riccardo on topic backmap problem: New molecule (ligand) (Updated)
Thank you and sorry for the slow follow-up.
Every particle in the CG and AA files must have different names, so that you can build a mapping file with unambiguous assignments - otherwise backward.py won't be able to determine which atom is mapped onto which bead. I think that's the problem.
In other words, try to modify your benzene itp file to :
################GRO.FILE############
benzene
3
1BENZ R1 1 1.383 1.453 1.515
1BENZ R2 2 1.520 1.625 1.515
1BENZ R3 3 1.597 1.424 1.470
3.00000 3.00000 3.00000
#######################################
and you need to use in the mapping files the atom names - highlighted below:
############## AA TOPOLOGY ############
...
[ moleculetype ]
; name nrexcl
BENZ 3
[ atoms ]
; nr type resnr residu atom cgnr charge mass
1 CG2R61 900 BNZ C3 1 -0.115 12.0110 ; qtot -0.115
2 CG2R61 900 BNZ C2 2 -0.115 12.0110 ; qtot -0.230
3 HGR61 900 BNZ H3 3 0.115 1.0080 ; qtot -0.115
4 HGR61 900 BNZ H2 4 0.115 1.0080 ; qtot 0.000
5 CG2R61 900 BNZ C1 5 -0.115 12.0110 ; qtot -0.115
6 CG2R61 900 BNZ C6 6 -0.115 12.0110 ; qtot -0.230
7 HGR61 900 BNZ H1 7 0.115 1.0080 ; qtot -0.115
8 HGR61 900 BNZ H6 8 0.115 1.0080 ; qtot 0.000
9 CG2R61 900 BNZ C5 9 -0.115 12.0110 ; qtot -0.115
10 CG2R61 900 BNZ C4 10 -0.115 12.0110 ; qtot -0.230
11 HGR61 900 BNZ H5 11 0.115 1.0080 ; qtot -0.115
12 HGR61 900 BNZ H4 12 0.115 1.0080 ; qtot 0.000
....
############## AA TOPOLOGY ############
So that your mapping file should look like this :
#############BENZ.CHARMM.MAP.file#######
[ molecule ]
BENZ
[ martini ]
R1 R2 R3
[ mapping ]
charmm36
[ atoms ]
1 C3 R1
2 C2 R1 R2
3 ....
.....
##############################
Every particle in the CG and AA files must have different names, so that you can build a mapping file with unambiguous assignments - otherwise backward.py won't be able to determine which atom is mapped onto which bead. I think that's the problem.
In other words, try to modify your benzene itp file to :
################GRO.FILE############
benzene
3
1BENZ R1 1 1.383 1.453 1.515
1BENZ R2 2 1.520 1.625 1.515
1BENZ R3 3 1.597 1.424 1.470
3.00000 3.00000 3.00000
#######################################
and you need to use in the mapping files the atom names - highlighted below:
############## AA TOPOLOGY ############
...
[ moleculetype ]
; name nrexcl
BENZ 3
[ atoms ]
; nr type resnr residu atom cgnr charge mass
1 CG2R61 900 BNZ C3 1 -0.115 12.0110 ; qtot -0.115
2 CG2R61 900 BNZ C2 2 -0.115 12.0110 ; qtot -0.230
3 HGR61 900 BNZ H3 3 0.115 1.0080 ; qtot -0.115
4 HGR61 900 BNZ H2 4 0.115 1.0080 ; qtot 0.000
5 CG2R61 900 BNZ C1 5 -0.115 12.0110 ; qtot -0.115
6 CG2R61 900 BNZ C6 6 -0.115 12.0110 ; qtot -0.230
7 HGR61 900 BNZ H1 7 0.115 1.0080 ; qtot -0.115
8 HGR61 900 BNZ H6 8 0.115 1.0080 ; qtot 0.000
9 CG2R61 900 BNZ C5 9 -0.115 12.0110 ; qtot -0.115
10 CG2R61 900 BNZ C4 10 -0.115 12.0110 ; qtot -0.230
11 HGR61 900 BNZ H5 11 0.115 1.0080 ; qtot -0.115
12 HGR61 900 BNZ H4 12 0.115 1.0080 ; qtot 0.000
....
############## AA TOPOLOGY ############
So that your mapping file should look like this :
#############BENZ.CHARMM.MAP.file#######
[ molecule ]
BENZ
[ martini ]
R1 R2 R3
[ mapping ]
charmm36
[ atoms ]
1 C3 R1
2 C2 R1 R2
3 ....
.....
##############################
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4 years 1 week ago #8492
by bhupendra123
Replied by bhupendra123 on topic backmap problem: New molecule (ligand) (Updated)
Thank you very much, Riccardo, for your kind reply.
This was very helpful. It worked.
Bhupendra
This was very helpful. It worked.
Bhupendra
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