Oh, you're right. Those are the contents of the tdb file. I wrote hdb by mistake! sorry! :-) Thanks so much Justin.
NOW, 1. I made an aminoacids.dat file and added FOR to other residues, as below: 49 ABU ACE AIB ALA ARG ARGN ASN ASN1 ASP ASP1 ASPH CYS CYS1 CYS2 CYSH DALA FOR GLN GLU GLUH GLY HIS HIS1 HISA HISB HISH HYP ILE LEU LYS LYSH MELEU MET MEVAL NAC NH2 PHE PHEH PHEU PHL PRO SER THR TRP TRPH TRPU TYR TYRH TYRU VAl 2. added FOR in .rtp file as before. but now, it doesn't recognize the FOR as the first residue! My protein has 25 residue but here 24 is written by gromacs. What's the problem? .dat file defined is wrong? 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
