[gmx-users] How to use "define = -DPOSRES" in Gromacs 2018?

[ZHANG Cheng]

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"<272699575 at qq.com>;
Date:  Mon, Jan 14, 2019 10:16 PM
To:  "gromacs.org_gmx-users"<gromacs.org_gmx-users at 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"<272699575 at qq.com>;
Date:  Mon, Jan 14, 2019 09:53 PM
To:  "gromacs.org_gmx-users"<gromacs.org_gmx-users at 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?