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Reverse CG with Amber
- xavier
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13 years 2 months ago #579
by xavier
Enjoy,
XAvier.
Replied by xavier on topic Reverse CG with Amber
Cool, so now you can get to the fun part!is wrote: The problem was with one of the top files.
I used command:
pdb2gmx -f aa.gro
to generate top files with mapping sections for protein and ligand. However, instead of that I got itp files: protein_A and protein_B with mapping sections for protein and IONS (should be for ligand), respectively.
Which caused all problems.
I fixed that and it works.
Thank you for your suggestions Xavier.
Enjoy,
XAvier.
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- andrzej
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13 years 2 months ago #581
by andrzej
Replied by andrzej on topic Reverse CG with Amber
Do not forget to put constraints on your protein dihedral angles.
Andrzej
Andrzej
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13 years 2 months ago #582
by xavier
What do you mean? Is this documented anywhere?
Replied by xavier on topic Reverse CG with Amber
andrzej wrote: Do not forget to put constraints on your protein dihedral angles.
Andrzej
What do you mean? Is this documented anywhere?
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- andrzej
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13 years 2 months ago #583
by andrzej
Replied by andrzej on topic Reverse CG with Amber
Documentation of all specific reverse options is in appendix of jcc paper
onlinelibrary.wiley.com/doi/10.1002/jcc.21415/abstract
however it looks like the same thing should be also on the website with the source
and maybe some additional information to make the procedure faster and easier
Andrzej
however it looks like the same thing should be also on the website with the source
and maybe some additional information to make the procedure faster and easier
Andrzej
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- is
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13 years 2 months ago #591
by is
Thanks, but it sounds like I will get more problems:)
Replied by is on topic Reverse CG with Amber
xavier wrote:
Cool, so now you can get to the fun part!is wrote: The problem was with one of the top files.
I used command:
pdb2gmx -f aa.gro
to generate top files with mapping sections for protein and ligand. However, instead of that I got itp files: protein_A and protein_B with mapping sections for protein and IONS (should be for ligand), respectively.
Which caused all problems.
I fixed that and it works.
Thank you for your suggestions Xavier.
Enjoy,
XAvier.
Thanks, but it sounds like I will get more problems:)
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13 years 2 months ago #592
by is
I will not, thank you.
Replied by is on topic Reverse CG with Amber
andrzej wrote: Do not forget to put constraints on your protein dihedral angles.
Andrzej
I will not, thank you.
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13 years 2 months ago #597
by is
Replied by is on topic Reverse CG with Amber
Hi Xavier,
So the 'fun part' just started...
As Andrzej mentioned, I should use g_dihfix to generate dihedral angle restraints. I used command:
g_dihfix -c aa.gro -p aa.top -fc 10 -o aa_restr.top.
and got quite common error (but I can't find solution to it):
Dihedral around X,Y not found in topology. Using mult=3
I searched gromacs mailing list and I found that there was problem with dihres.c in version 3.2., but that was fixed before release of 3.3.
So I guess that doesn't apply any more.
What else can cause this error, and how to fix it?
Maybe It is my mapping section?:)
Thank you in advance for your help.
is
So the 'fun part' just started...
As Andrzej mentioned, I should use g_dihfix to generate dihedral angle restraints. I used command:
g_dihfix -c aa.gro -p aa.top -fc 10 -o aa_restr.top.
and got quite common error (but I can't find solution to it):
Dihedral around X,Y not found in topology. Using mult=3
I searched gromacs mailing list and I found that there was problem with dihres.c in version 3.2., but that was fixed before release of 3.3.
So I guess that doesn't apply any more.
What else can cause this error, and how to fix it?
Maybe It is my mapping section?:)
Thank you in advance for your help.
is
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- andrzej
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13 years 2 months ago #598
by andrzej
Replied by andrzej on topic Reverse CG with Amber
Hey
The flow of the process is:
1 pdb2gmx for protein chain (proteins) to include mappings
2 g_dihfix to include additional section [dihedral_restraints] for each protein. This affects the molecule definition so should be done for each protein itp file separately
3 put all information about molecules together in a final aa topology file
4 g_fg2cg to generate initial "random" structure
5 mdrun
Did you put your constarints to the itp files of protein_a and protein_b
?
Andrzej
The flow of the process is:
1 pdb2gmx for protein chain (proteins) to include mappings
2 g_dihfix to include additional section [dihedral_restraints] for each protein. This affects the molecule definition so should be done for each protein itp file separately
3 put all information about molecules together in a final aa topology file
4 g_fg2cg to generate initial "random" structure
5 mdrun
Did you put your constarints to the itp files of protein_a and protein_b
?
Andrzej
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- is
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13 years 2 months ago #599
by is
Yes. Thank you for your answer. Splitting gro file was crucial to generate dihedral restraints. Everything is working now. I'm currently testing different temperatures for SA.
Again thank you Andrzej and Xavier for your help.
is
Replied by is on topic Reverse CG with Amber
andrzej wrote: Hey
The flow of the process is:
1 pdb2gmx for protein chain (proteins) to include mappings
2 g_dihfix to include additional section [dihedral_restraints] for each protein. This affects the molecule definition so should be done for each protein itp file separately
3 put all information about molecules together in a final aa topology file
4 g_fg2cg to generate initial "random" structure
5 mdrun
Did you put your constarints to the itp files of protein_a and protein_b
?
Andrzej
Yes. Thank you for your answer. Splitting gro file was crucial to generate dihedral restraints. Everything is working now. I'm currently testing different temperatures for SA.
Again thank you Andrzej and Xavier for your help.
is
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