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? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.