After checking the topology of my peptide, I found that every term in the cMAP section involve three consecutive residues. So I guess no cMAP term is required for di-ALA. Jianguo
--- On Mon, 10/10/11, César Ávila <clav...@gmail.com> wrote: From: César Ávila <clav...@gmail.com> Subject: Re: [gmx-users] CMAP for alanine dipeptide in Charmm27 ff To: "Jianguo Li" <ljg...@yahoo.com.sg>, "Discussion list for GROMACS users" <gmx-users@gromacs.org> Date: Monday, 10 October, 2011, 5:51 PM v4.5.4 As I commented above, I had to manually add an entrance for the cmap terms in the topology file as pdb2gmx would not generate them for the alanine dipeptide. There seems to be no problem for larger peptides. Cheers Cesar 2011/10/10 Jianguo Li <ljg...@yahoo.com.sg> which gromacs version are you using? cMAP is implemented in v4.5 or later Jianguo From: César Ávila <clav...@gmail.com> To: Discussion list for GROMACS users <gmx-users@gromacs.org> Sent: Sunday, 9 October 2011 12:07 AM Subject: [gmx-users] CMAP for alanine dipeptide in Charmm27 ff I would like to run REMD simulations on the alanine dipeptide using the Charmm27ff + CMAP. Still, after processing the pdb with pdb2gmx, I do not see any entrance referring to the cmap term in the topology file. Does this mean that Cmap won't be calculated? -- gmx-users mailing list gmx-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 list gmx-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 list gmx-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
