Re: [gmx-users] Definiting protonation in pdb2gmx input
Quoting Justin Lemkul : problem. Please file a bug report on Redmine and include example input files and pdb2gmx syntax you're using. Ok, thanks. Bug posted at https://redmine.gromacs.org/issues/2480 -- 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.
Re: [gmx-users] Definiting protonation in pdb2gmx input
On 4/16/18 9:44 AM, mhuht...@abo.fi wrote: Quoting Justin Lemkul : I just tested this in GROMACS 2018 and it works fine - if you provide the protonated residue name, pdb2gmx correctly interprets the protonation state. Do you have a use case that fails? Is this behavior documented somewhere? I don't seem to find any mention of it. It's always been default behavior - if pdb2gmx matches a residue name, it processes the coordinates according to the .rtp file. My initial problem was that when I attempted to use a structure with hydrogens (polar only) as input, I just got a lot of error messages about atom names and the numbers of atoms not matching the residue topology, which made me assume that pdb2gmx simply does not do the trick. As you mention below, you're using a UA force field, which won't have most of the H atoms you are supplying, so you'll get errors. Using -ignh should fix that (but then again, see below). Now I did a bit more testing, and at least renaming ASP to ASPH in the input will get me an ASPH in the output, but only the residue name, not the hydrogen. So I get a residue named ASPH, but the structure is an unprotonated ASP. Is this a bug? Or is pdb2gmx expecting to find the hydrogen atom line in the input? All necessary hydrogens should be reconstructed according to the .hdb file (for which entries for protonated amino acids exist and are functional). Then I tried changing a HIS to HISA, and that one works. By default, pdb2gmx adds two hydrogens to that histidine, but with HISA specified, I do get only the hydrogen on ND, as expected. This is all using Gromacs 2018 and specifying GROMOS96 54a7, and modifying a crystal structure PDB file taken from the PDB, with no hydrogens. There does appear to be a problem specifically with united-atom force fields. Both CHARMM and AMBER function correctly, with or without -ignh. Using any GROMOS variant, with or without -ignh leads to a problem. Please file a bug report on Redmine and include example input files and pdb2gmx syntax you're using. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- 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.
Re: [gmx-users] Definiting protonation in pdb2gmx input
Quoting Justin Lemkul : I just tested this in GROMACS 2018 and it works fine - if you provide the protonated residue name, pdb2gmx correctly interprets the protonation state. Do you have a use case that fails? Is this behavior documented somewhere? I don't seem to find any mention of it. My initial problem was that when I attempted to use a structure with hydrogens (polar only) as input, I just got a lot of error messages about atom names and the numbers of atoms not matching the residue topology, which made me assume that pdb2gmx simply does not do the trick. Now I did a bit more testing, and at least renaming ASP to ASPH in the input will get me an ASPH in the output, but only the residue name, not the hydrogen. So I get a residue named ASPH, but the structure is an unprotonated ASP. Is this a bug? Or is pdb2gmx expecting to find the hydrogen atom line in the input? Then I tried changing a HIS to HISA, and that one works. By default, pdb2gmx adds two hydrogens to that histidine, but with HISA specified, I do get only the hydrogen on ND, as expected. This is all using Gromacs 2018 and specifying GROMOS96 54a7, and modifying a crystal structure PDB file taken from the PDB, with no hydrogens. -- 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.
Re: [gmx-users] Definiting protonation in pdb2gmx input
On 4/16/18 7:07 AM, mhuht...@abo.fi wrote: One of the recurring questions on the list seems to be how to define residue protonation states non-interactively in pdb2gmx input. The interactive options are a bit of a nightmare to use. Could pdb2gmx be modified to optionally read the residue types from the PDB file itself? The user would replace e.g. "ASP " with "ASPH" in the PDB file, and pdb2gmx would build a protonated aspartate, whether the hydrogen atom is there in the PDB file or not. Same for all residue types, of course. The upside would be having readable and more easily scriptable input instead of trying to script the interactive input. I realize that the names of the residue types differ between force fields, but even requiring force field specific names would be ok as far as I'm concerned (ASPH in Gromos, ASH in Amber, etc.). I just tested this in GROMACS 2018 and it works fine - if you provide the protonated residue name, pdb2gmx correctly interprets the protonation state. Do you have a use case that fails? -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- 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.
