I tried again as below: 1. defined FOR in .rtp file 2. defined FOR in aminoacids.dat file. 3. chose NH2 as N-Terminal
and then got this topology for FOR and VAL: ; residue 0 FOR rtp FOR q 0.0 1 CH1 0 FOR C 1 0.38 13.019 ; qtot 0.38 2 O 0 FOR O 1 -0.38 15.9994 ; qtot 0 ; residue 1 VAL rtp VAL q 0.0 3 NL 1 VAL N 2 -0.83 14.0067 ; qtot -0.83 4 H 1 VAL H1 2 0.415 1.008 ; qtot -0.415 5 H 1 VAL H2 2 0.415 1.008 ; qtot 0 6 CH1 1 VAL CA 3 0 13.019 ; qtot 0 7 CH1 1 VAL CB 4 0 13.019 ; qtot 0 8 CH3 1 VAL CG1 5 0 15.035 ; qtot 0 9 CH3 1 VAL CG2 6 0 15.035 ; qtot 0 10 C 1 VAL C 7 0.38 12.011 ; qtot 0.38 11 O 1 VAL O 7 -0.38 15.9994 ; qtot 0 I guess the topology is correct. Isn't it? 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 7:17 PM Subject: Re: [gmx-users] H-atoms in .hdb file On 6/26/12 10:44 AM, Shima Arasteh wrote: > > > Thanks for you reply. > As I explained befor, I need to add a formyl residue to the gmx.ff . I > defined it in aminoacid.rtp file and aminoacid.n.tdb . > > In .rtp file: > > [ atoms ] > C CH1 0.380 0 > O O -0.380 0 > [ bonds ] > C O > C +N > [angles ] > ai aj ak > O C +N > [ dihedrals ] > O C +N +CA > > In .n.hdb file: > > [ replace ] > C CH1 0.380 0 > O O -0.380 0 > [ bonds ] > C O > C +N These are the contents of a .n.tdb file, as .n.hdb files do not exist. You also do not need such modifications. If you have the formyl group in the .rtp file, and it is appropriately defined as "Protein" in residuetypes.dat, then all you need to do is choose "None" for the N-terminus of the protein. > > The first residue after formyl is VAL. I know when VAL is added to FOR, a > peptide bond is formed and 1 H-atom is added to the N-atom in this bonding, > this H-atom is already defined in .hdb file. > In my case, an error ( missing H on VAL residue) is occured, thus I decieded > to add the H by hand in pdb file. > The error probably comes from an incorrect assignment of terminus state. -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
