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? Sincerely, Shima ----- Original Message ----- From: Justin A. Lemkul <jalem...@vt.edu> To: Shima Arasteh <shima_arasteh2...@yahoo.com>; Discussion list for GROMACS users <gmx-users@gromacs.org> Cc: Sent: Wednesday, June 27, 2012 2:58 PM Subject: Re: [gmx-users] H-atoms in .hdb file On 6/27/12 3:38 AM, Shima Arasteh wrote: > > > As Justin suggested me, I added the FOR residue to the .rtp file of FF and > then added the FOR as a protein in residuetypes.dat . FOR is the first > residue in protein chain. I chose none as the N-terminus . But after > processing the .pdb file the FOR is identified itself but "not" identified as > protein. > How so? What line did you add to residuetypes.dat, and what was the exact problematic output of pdb2gmx? -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
