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Generating mapping with pdb2gmx
- nina
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13 years 5 months ago #433
by nina
Generating mapping with pdb2gmx was created by nina
Hello,
I used Martini ff to do a MD on a protein in water, and now I am interested in converting the last coarse grained conformation obtained after the MD into an all-atom representation.
I have done the reverse transformation for the peptide walp spanning the DPPC bilayer and everything went well. So now I am trying to do the same with my protein. I am using pdb2gmx to create a fg.top file similar to the one found in the tutorial with the mapping section, but I am having some problems with that.
When I give as input the all-atom pdb file to pdb2gmx and choose the force field with [mapping] option it always gives me the following error:
Atom H not found in residue 1 while adding mapping
I tried using a .gro structure and the same thing happens.
I am really sorry to bother you, but I can't seem to find a solution to this.
What I realised is that in the empty topology created the parametres included are :
; Include forcefield parameters
#include "ffG53a6m.itp
whereas in the fg.top of the tutorial the one taken is in the top directory (top/ffDPPC.itp)
Does this have something to do with it?
Thank you very much for your help
I used Martini ff to do a MD on a protein in water, and now I am interested in converting the last coarse grained conformation obtained after the MD into an all-atom representation.
I have done the reverse transformation for the peptide walp spanning the DPPC bilayer and everything went well. So now I am trying to do the same with my protein. I am using pdb2gmx to create a fg.top file similar to the one found in the tutorial with the mapping section, but I am having some problems with that.
When I give as input the all-atom pdb file to pdb2gmx and choose the force field with [mapping] option it always gives me the following error:
Atom H not found in residue 1 while adding mapping
I tried using a .gro structure and the same thing happens.
I am really sorry to bother you, but I can't seem to find a solution to this.
What I realised is that in the empty topology created the parametres included are :
; Include forcefield parameters
#include "ffG53a6m.itp
whereas in the fg.top of the tutorial the one taken is in the top directory (top/ffDPPC.itp)
Does this have something to do with it?
Thank you very much for your help
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- andrzej
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13 years 5 months ago #435
by andrzej
Replied by andrzej on topic Generating mapping with pdb2gmx
pdb2gmx -ignh -missing
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- nina
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13 years 5 months ago #436
by nina
Replied by nina on topic Generating mapping with pdb2gmx
Thank you very much!!!!
It works perfectly!
It works perfectly!
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