[gmx-users] Simulation of protein at specific pH
Dear Gromacs User, I want to simulate my protein at a specific pH. Using H++ server I have generated my .pdb file at pH 5. But pdb2gmx is showing all the usual fatal error like Atom HB3 in residue MET 1 not found in rtp entry with 17 atoms. But I can't use -ignh option, because it is bringing back at the same normal stage. So what should I do I want to carry out simulation at pH 5. Thanks Prerna -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Simulation of protein at specific pH
prerna bhardwaj wrote: Dear Gromacs User, I want to simulate my protein at a specific pH. Using H++ server I have generated my .pdb file at pH 5. But pdb2gmx is showing all the usual fatal error like Atom HB3 in residue MET 1 not found in rtp entry with 17 atoms. But I can't use -ignh option, because it is bringing back at the same normal stage. So what should I do I want to carry out simulation at pH 5. It sounds like you should indeed be using -ignh because you have a malformed input. Under no conditions should the beta-carbon of methionine ever have three protons. Carbon atoms can't have five bonds. Either the atom naming in your .pdb file is wrong (which will cause pdb2gmx to fail) or the protonation state is wrong (which will cause pdb2gmx to fail in the absence of -ignh). You can set the protonation state of any titratable residues and termini using pdb2gmx -inter, in concert with -ignh, which appears to be necessary in your case. -Justin Thanks Prerna -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Simulation of protein at specific pH
Thank you so much Justin, that really helped :) On Mon, Apr 25, 2011 at 12:17 AM, Justin A. Lemkul jalem...@vt.edu wrote: prerna bhardwaj wrote: Dear Gromacs User, I want to simulate my protein at a specific pH. Using H++ server I have generated my .pdb file at pH 5. But pdb2gmx is showing all the usual fatal error like Atom HB3 in residue MET 1 not found in rtp entry with 17 atoms. But I can't use -ignh option, because it is bringing back at the same normal stage. So what should I do I want to carry out simulation at pH 5. It sounds like you should indeed be using -ignh because you have a malformed input. Under no conditions should the beta-carbon of methionine ever have three protons. Carbon atoms can't have five bonds. Either the atom naming in your .pdb file is wrong (which will cause pdb2gmx to fail) or the protonation state is wrong (which will cause pdb2gmx to fail in the absence of -ignh). You can set the protonation state of any titratable residues and termini using pdb2gmx -inter, in concert with -ignh, which appears to be necessary in your case. -Justin Thanks Prerna -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Simulation of protein at specific pH
On 2011-04-24 20.47, Justin A. Lemkul wrote: prerna bhardwaj wrote: Dear Gromacs User, I want to simulate my protein at a specific pH. Using H++ server I have generated my .pdb file at pH 5. But pdb2gmx is showing all the usual fatal error like Atom HB3 in residue MET 1 not found in rtp entry with 17 atoms. But I can't use -ignh option, because it is bringing back at the same normal stage. So what should I do I want to carry out simulation at pH 5. It sounds like you should indeed be using -ignh because you have a malformed input. Under no conditions should the beta-carbon of methionine ever have three protons. Carbon atoms can't have five bonds. It doesn't have three protons but the official (IUPAC/IUPAB) side chain atom naming is: CG (counts as 1) HB2 HB3, so the H++ server is correct, and the braindead force fields are wrong. Either the atom naming in your .pdb file is wrong (which will cause pdb2gmx to fail) or the protonation state is wrong (which will cause pdb2gmx to fail in the absence of -ignh). You can set the protonation state of any titratable residues and termini using pdb2gmx -inter, in concert with -ignh, which appears to be necessary in your case. -Justin Thanks Prerna -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Virtual site at COM of more than 4 atoms
Hi I am not sure , even after reading the manual, about how to specify virtual site in topology file which is located at com of 5 atoms. If I were to specify it by using [ virutal_sitesn] then how to specify weights, so that vsite is at COM? thanks sikandar -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
