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Backmapping a new molecule
- P_Banerjee
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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
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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- riccardo
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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.
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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- P_Banerjee
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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
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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- riccardo
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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:
##########################################################################
Then your "topol_AA.top" must look like this (note the order of residues in the [molecules] section, answering your point (b)):
##########################################################################
And your "EBEN_opls.itp" should look like this (note the residue names matching the ones in the "CG.gro", answering your point (a)):
#####################################
#####################################
Hope this helps!
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
Best,
Pallavi
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