Re: [gmx-users] residues in force fields
Hi Suggestions at http://www.gromacs.org/Documentation/File_Formats/Coordinate_File Mark On Sat, Jan 31, 2015 at 11:35 PM, shahab shariati shahab.shari...@gmail.com wrote: Dear Mark Thanks for your answer. I have a pdb file. If I want to cap N- and C-terminal with ACE and NME, respectively, what to do? Is there an specific software for that? Best wishes, Shahab -- 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.
[gmx-users] residues in force fields
Dear all I am a beginner in gromacs. I am studying manual and force fields. I have a question about 2 residue name in aminoacid.rtp file in force fields (for example, amber03). I want to know ACE and NME residues. Any help will highly appreciated. -- 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] residues in force fields
Hi, Those are for acetyl and N-methylamine chemical moieties. Those are often used to cap peptide fragments to avoid zwitterions (both in simulation and experiment). Mark On Sat, Jan 31, 2015 at 9:24 PM, shahab shariati shahab.shari...@gmail.com wrote: Dear all I am a beginner in gromacs. I am studying manual and force fields. I have a question about 2 residue name in aminoacid.rtp file in force fields (for example, amber03). I want to know ACE and NME residues. Any help will highly appreciated. -- 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.
[gmx-users] residues in force fields
Dear Mark Thanks for your answer. I have a pdb file. If I want to cap N- and C-terminal with ACE and NME, respectively, what to do? Is there an specific software for that? Best wishes, Shahab -- 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.
