normal Backmapping a new molecule

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3 years 11 months ago #8491 by P_Banerjee
Backmapping a new molecule was created by P_Banerjee
Hello MARTINI community,

I want to backmap my coarse-grained MARTINI system of protein and glycolipid embedded in bilayer to the all-atom resolution using backward.py. From the tutorial, I gather that one needs to provide the force-field as an option in the command. The problem is I have a new molecule ( previously undefined in MARTINI), as well as a customized atomistic force-field. How possible is it to use backward.py and initram.sh to backmap such a system?

Any input would be much appreciated!

Thanks.

Best,
Pallavi

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3 years 11 months ago #8493 by riccardo
Replied by riccardo on topic Backmapping a new molecule
First of all, I would recommend going through Backward's tutorial  cgmartini.nl/index.php/tutorials-general...others-gmx5#Backward , if you haven't already done so.

Secondly, if you have a "new" molecule, that is, a molecule for which no mapping file is available, but you do have an atomistic force field, then you need to:

1. Create the mapping file. You can obtain a mapping file from jbarnoud.github.io/cgbuilder/ by uploading the AA structure of your force field (what you want is the order of atoms in the AA structure you upload to be the same as the one in your AA FF, of course!). The GUI is pretty intuitive. Also, maybe useful to check out this thread involving a "new" small-molecule for which a mapping file had to be written up (in particular, see my post number "#8489"):  cgmartini.nl/index.php/component/kunena/...-ligand-updated#8489

2. Backmap. You can then give a try to backward (use the latest version available here: github.com/tsjerk/backward ). In case of problems, start debugging by backmapping 1 molecule (your "new" molecule)  in vacuum and grow in complexity from there.

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3 years 11 months ago #8494 by P_Banerjee
Replied by P_Banerjee on topic Backmapping a new molecule
Thank you for the explanation, Riccardo!

I did follow the tutorial, and now have a better understanding of the methodology. Backmapping a new molecule would entail creating a new mapping file.
However, I have another nagging concern. In the tutorial, the following is mentioned: "topol.top, which contains the molecules in the same order they are present in CG_posre.gro and with the same names." In order to run backward.py, is it important that:
(a) the residue names in the CG.gro should match those in the target atomistic topology?
(b) the order of residues in the CG.gro input structure file and that in the target atomistic topology file be the same?

Best,
Pallavi

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3 years 11 months ago #8495 by riccardo
Replied by riccardo on topic Backmapping a new molecule
Let me clear your doubts (I hope) with one example. Let's say that your system consists of 1 ethyl-benzene and 1 toluene molecules solvated in 200 chloroform molecules.

Then, let's say that your "CG.gro" (= file to be backmapped) specifically looks like this:


#####################################
Two molecules in a solvent
  889
    1EBEN    R1    1   1.343   3.579   4.245 
    1EBEN    R2    2   1.197   3.802   4.131 
    1EBEN    R3    3   1.145   3.532   4.039 
    1EBEN    R4    4   1.037   3.746   3.891  
    2CLF     CX    5   2.741   3.468   1.864 
    3CLF     CX    6   2.043   2.116   3.094
    4...........
  201CLF     CX  201   3.352   2.073   2.961 
  202TOLU    R1  202   5.129   3.231   2.820  
  202TOLU    R2  203   5.250   2.958   2.849  
  202TOLU    R3  204   4.967   2.985   2.877 
   4.73822   4.73822   4.73822
#####################################


Then your "topol_AA.top" must look like this (note the order of residues in the [molecules] section, answering your point (b)):

#####################################
; Include forcefield parameters
#include "oplsaa.ff/forcefield.itp"

; Include chain topologies
#include "EBEN_opls.itp"
#include "TOLU_opls.itp"
#include "CLF_opls.itp"

[ system ]
; Name
Two molecules in water

[ molecules ]
; Compound        #mols
EBEN                     1
CLF                   200
TOLU                     1
#####################################

And your "EBEN_opls.itp" should look like this (note the residue names matching the ones in the "CG.gro", answering your point (a)):

#####################################
....
[ moleculetype ]
; Name               nrexcl
EBEN                  3
[ atoms ]
;   nr       type  resnr residue  atom   cgnr     charge       mass
     1   opls_800      1    EBEN  C00      1    -0.2326    12.0110
     2   opls_801      1    EBEN  C01      1    -0.1364    12.0110
     3   opls_802      1    EBEN  C02      1    -0.0797    12.0110
........
#####################################

Hope this helps!

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3 years 11 months ago #8496 by P_Banerjee
Replied by P_Banerjee on topic Backmapping a new molecule
Thanks a lot for this coherent explanation, Riccardo! Yes, my doubts are cleared now.

Best,
Pallavi

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