normal tutorial example

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9 years 4 months ago #668 by silvina
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Hi,

I am learning on how to use the martini ff for proteins, I have succesfully prepared all the input files for the simulation of ubiquitin and I was able to run the simulations. However, when I've tried to perform the simulation of the second protein that is inside the directory proteins/ the 1a8g protein that is a dimer. I was able to run the scripts atom2cg_v2.1.awk, dssp2ssd.py and seq2itp.pl without problems. Then when I try to run grompp to generate the *.trp file to do the minimization I get the following error messdage: "number of coordinates in coordinate file does not match topology". I believe the issue is that this protein is a dimer. In the topology file I did the following:

#include "martini_v2.1.itp"
#include "1a8g.itp"
[ system ]
; Name
HIV-1 PROTEASE

[ molecules ]
; Compound #mols
Protein 1

When I looked into the output of atom2cg_v2.1.awk I see that now the information of the chain is lost, if it is chain A or B. Could this be the issue? How gromacs will know that the system has 2 chains if this information is removed with atom2cg_v2.1.awk? Any ideas on how to solve it?

Thanks in advance!

Silvina

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9 years 4 months ago #669 by xavier
Replied by xavier on topic tutorial example

silvina wrote: Hi,

I am learning on how to use the martini ff for proteins, I have succesfully prepared all the input files for the simulation of ubiquitin and I was able to run the simulations. However, when I've tried to perform the simulation of the second protein that is inside the directory proteins/ the 1a8g protein that is a dimer. I was able to run the scripts atom2cg_v2.1.awk, dssp2ssd.py and seq2itp.pl without problems. Then when I try to run grompp to generate the *.trp file to do the minimization I get the following error messdage: "number of coordinates in coordinate file does not match topology". I believe the issue is that this protein is a dimer. In the topology file I did the following:


#include "martini_v2.1.itp"
#include "1a8g.itp"
[ system ]
; Name
HIV-1 PROTEASE

[ molecules ]
; Compound #mols
Protein 1

When I looked into the output of atom2cg_v2.1.awk I see that now the information of the chain is lost, if it is chain A or B. Could this be the issue? How gromacs will know that the system has 2 chains if this information is removed with atom2cg_v2.1.awk? Any ideas on how to solve it?

Thanks in advance!

Silvina


You can check your protein topology and see what is in there ... did you make a topology for the dimer of for one monomer only?

gromacs will not know that there two proteins if you do not tell it is so ... youi should basically do the topology for a monomer and then define that there are two proteins in the system.

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