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 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. Any suggestion please? Thanks so much. Sincerely, Shima ----- Original Message ----- From: Justin A. Lemkul <[email protected]> To: Shima Arasteh <[email protected]>; Discussion list for GROMACS users <[email protected]> Cc: Sent: Tuesday, June 26, 2012 6:58 PM Subject: Re: [gmx-users] H-atoms in .hdb file On 6/26/12 10:25 AM, Shima Arasteh wrote: > > > Dear gmx users, > > However this H-atom is defined in .hdb file of force field before, why > sometimes I need to add a H-atom to the pdb on my own? > > A properly constructed .hdb entry eliminates the need for manual introduction of H atoms. If you aren't achieving the desired behavior, you will have to be a lot more specific about what you're doing and what you're observing. -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 [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
