Dear Cheng: You can define protonation states like this:
echo "0 1 2" | pdb2gmx -ff amber99sb-ildn -water tip3p -his That will give you, in order for three HIS residues: 0. H on ND1 only (HID) 1. H on NE2 only (HIE) 2. H on ND1 and NE2 (HIP) You can also use -inter, but you'll need to do a dry-run to see what order gmx asks you for these things in. From my tests, it follow an order that is first residue type (in order: LYS, ARG, GLN, ASP, GLU, HIS, disulfide bonds) and for each of these, order by residue number. Chris. ________________________________________ From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Zhang, Cheng <c.zhang...@ucl.ac.uk> Sent: 21 May 2015 10:38 To: gromacs.org_gmx-users@maillist.sys.kth.se Cc: Zhang, Cheng Subject: [gmx-users] pdb2gmx: can we use a file to specify the protonation instead of using "-inter"? Dear GROMACS experts, Can I ask is there a more efficient way to deal with the "-inter" option in the pdb2gmx command? Now, I have to manually assign individual protonation status one by one, which takes a very long time. Sometimes I make a mistake and I have to re-do all of them again. Would it be possible if the command line can link to a file, which specifies the protonation for individual residues? Thank you very much. Yours sincerely Cheng -- 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. -- 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.
