[gmx-users] How to change the protonation state of an aminoacid in a peptide
Hi. I have the gro file for a peptide in vacuum, in the peptide, there is only one ASP, and I want to change it to ASPH. If I run pdb2gmx -asp and select the protonated state, the only change is in the name of the residue (it doesn't add the needed hydrogen). Is there any automatic way changing the protonated state for this residue? Thanks in advance -- Camilo Andrés Jiménez Cruz ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] How to change the protonation state of an aminoacid in a peptide
Camilo Andrés Jimenez Cruz wrote: Hi. I have the gro file for a peptide in vacuum, in the peptide, there is only one ASP, and I want to change it to ASPH. If I run pdb2gmx -asp and select the protonated state, the only change is in the name of the residue (it doesn't add the needed hydrogen). Is there any automatic way changing the protonated state for this residue? Well, the command that you entered should have worked (it always has for me). As for getting any extra advice, you will have to provide a much more complete description, including the following: 1. Which force field you are trying to use 2. Relevant output (from screen and from the structure/topology) 3. Which Gromacs version you are using 4. Any relevant details on compiler types, computer system, and how Gromacs was compiled -Jusitn Thanks in advance -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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/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/mailing_lists/users.php
Re: [gmx-users] How to change the protonation state of an aminoacid in a peptide
I already found the problem, Thanks! The point is that I was using a non standard forcefield, In this forcefield, the protonated state is called ASH. the program tried to find the ASPH and as it couldn't it didn't changed anything. Thanks again! On Wed, Jul 29, 2009 at 4:53 PM, Justin A. Lemkuljalem...@vt.edu wrote: Camilo Andrés Jimenez Cruz wrote: Hi. I have the gro file for a peptide in vacuum, in the peptide, there is only one ASP, and I want to change it to ASPH. If I run pdb2gmx -asp and select the protonated state, the only change is in the name of the residue (it doesn't add the needed hydrogen). Is there any automatic way changing the protonated state for this residue? Well, the command that you entered should have worked (it always has for me). As for getting any extra advice, you will have to provide a much more complete description, including the following: 1. Which force field you are trying to use 2. Relevant output (from screen and from the structure/topology) 3. Which Gromacs version you are using 4. Any relevant details on compiler types, computer system, and how Gromacs was compiled -Jusitn Thanks in advance -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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 list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Camilo Andrés Jiménez Cruz ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
