Thank you Mark!
The "Protein_A.itp" is obtained by:
python martinize.py -f 1UBQ.pdb -o single-ubq.top -x 1UBQ-CG.pdb -dssp
./dssp-2.0.4-linux-amd64 -p backbone -ff martini22
So the "Protein_A.itp" has the restraints in the "1UBQ-CG.pdb".
So I should use "-r 1UBQ-CG.pdb"?
So the whole command is the below?
gmx grompp -p system.top -r 1UBQ-CG.pdb -c solvated.gro -f minimization.mdp -o
minimization.tpr
------------------ Original ------------------
From: "ZHANG Cheng"<272699...@qq.com>;
Date: Mon, Jan 14, 2019 10:16 PM
To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>;
Subject: Re: How to use "define = -DPOSRES" in Gromacs 2018?
Thank you Mark!
Sorry, I do not have a "targetcoords.gro" for the grompp.
I was trying to use
"gmx grompp -p system.top -c solvated.gro -f minimization.mdp -o
minimization.tpr",
and the "system.top" has a line of " #include "Protein_A.itp" ",
and the "Protein_A.itp" file has the restraints I need.
Should I modify the "minimization.mdp" instead?
------------------ Original ------------------
From: "ZHANG Cheng"<272699...@qq.com>;
Date: Mon, Jan 14, 2019 09:53 PM
To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>;
Subject: How to use "define = -DPOSRES" in Gromacs 2018?
My backbone restraints is shown in the "Protein_A.itp" file:
#ifdef POSRES
#ifndef POSRES_FC
#define POSRES_FC 1000.00
#endif
[ position_restraints ]
1 1 POSRES_FC POSRES_FC POSRES_FC
3 1 POSRES_FC POSRES_FC POSRES_FC
5 1 POSRES_FC POSRES_FC POSRES_FC
......
162 1 POSRES_FC POSRES_FC POSRES_FC
163 1 POSRES_FC POSRES_FC POSRES_FC
#endif
The Martini protein tutorial said: specify "define = -DPOSRES" in the mdp file
for "gmx grompp".
However, adding "define = -DPOSRES" to the mdp file causes the error:
Fatal error:
Cannot find position restraint file restraint.gro (option -r).
>From GROMACS-2018, you need to specify the position restraint coordinate files
explicitly to avoid mistakes, although you can still use the same file as you
specify for the -c option.
The tutorial uses Gromacs 5, but I am using Gromacs 2018. Is this the problem
for that?
How can I trigger those restraints in "Protein_A.itp" file using Gromacs 2018?
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