Anyway, thanks for your reply . I appreciate you. Sincerely, Shima
Sincerely, Shima ________________________________ From: Justin A. Lemkul <jalem...@vt.edu> To: Discussion list for GROMACS users <gmx-users@gromacs.org> Sent: Wednesday, June 27, 2012 3:54 PM Subject: Re: [gmx-users] H-atoms in .hdb file On 6/27/12 6:38 AM, Shima Arasteh wrote: > > > I added this line to the residuetypes.dat file: > FOR Protein > > Then running this command: > pdb2gmx -f protein.pdb -water spc -ter > > Written as blow: > > Processing chain 1 (177 atoms, 25 residues) > Warning: Starting residue FOR0 in chain not identified as Protein/RNA/DNA. > Identified residue VAL1 as a starting terminus. > Identified residue GLY24 as a ending terminus. > > Asked for terminus: > I chose "none" as the N-terminus. > > Getting this: > Processing chain 1 (177 atoms, 25 residues) > Warning: Starting residue FOR0 in chain not identified as Protein/RNA/DNA. > Identified residue VAL1 as a starting terminus. > Identified residue GLY24 as a ending terminus. > 8 out of 8 lines of specbond.dat converted successfully > Select start terminus type for VAL-1 > 0: NH3+ > 1: NH2 > 2: None > 2 > Start terminus VAL-1: None > Select end terminus type for GLY-24 > 0: COO- > 1: COOH > 2: None > 0 > End terminus GLY-24: COO- > > ------------------------------------------------------- > Program pdb2gmx, VERSION 4.5.5 > Source code file: > /home/abuild/rpmbuild/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c, line: 1035 > > Fatal error: > There is a dangling bond at at least one of the terminal ends. Select a > proper terminal entry. > > > Would you helping me with it with your useful suggestions? > I honestly have no idea why that's not working. It's the exact same workflow used with all other capping groups and I use it routinely. -Justin -- ======================================== Justin A. Lemkul, Ph.D. Research Scientist 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-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 * Only plain text messages are allowed! * 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
