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.
Any suggestion please? Thanks in advance Sincerely, Shima ________________________________ From: Mark Abraham <mark.abra...@anu.edu.au> To: Shima Arasteh <shima_arasteh2...@yahoo.com> Sent: Wednesday, June 27, 2012 11:54 AM Subject: Re: [gmx-users] H-atoms in .hdb file On 27/06/12, Shima Arasteh <shima_arasteh2...@yahoo.com> wrote: I added the FOR residue as protein in residuetypes.dat file, but still says it's not identified as protein/DNA/RNA. > >Would you mind helping me with your suggestions? Apparently it's not been done right, but we don't have enough detail about what you've done to know what you've done wrong. Look carefully at the contents of the file you changed, and inspect your output carefully for clues. Mark > >Thanks in advance > > >Sincerely, >Shima > > >----- Original Message ----- >From: Justin A. Lemkul <jalem...@vt.edu> >To: Discussion list for GROMACS users <gmx-users@gromacs.org> >Cc: >Sent: Tuesday, June 26, 2012 8:20 PM >Subject: Re: [gmx-users] H-atoms in .hdb file > > > >On 6/26/12 11:47 AM, Shima Arasteh wrote: >> OK, but when I chose none, it gives me a fatal error ( dangling bond! ). A >> new problem! So how do I solve it? >> > >"Dangling bond" errors were introduced as part of the output in Gromacs 4.5. >The "aminoacids.dat" file was only used by older (4.0.x and earlier) versions >of Gromacs. You need to be modifying "residuetypes.dat" to indicate that FOR >is a Protein residue so that the chain is continuous with respect to its >content type. > >http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field > >-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 >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
