Dear Justin, Your suggestion of defining FVAL worked properly and at last I got the topology! :) Thanks a llllllllllllllllooooooooooooooooooooooooooottttttttttttttttttttt! :)
APPRECIATE YOU! Sincerely, Shima ----- Original Message ----- From: Justin A. Lemkul <jalem...@vt.edu> To: Discussion list for GROMACS users <gmx-users@gromacs.org> Cc: Sent: Thursday, June 28, 2012 12:17 AM Subject: Re: [gmx-users] Re: pdb2gmx error On 6/27/12 2:42 PM, Shima Arasteh wrote: > You are right. > > OK, the reason of adding FOR is what I explained a few minutes ago. > All over, I'm supposed to use a modern FF . ( In similar researches I found > CHARMM is suitable, so I would add FOR as the procedure explained in > GROMACS.ORG) > This sounds like a good idea. > For now, because I wanna regenerate an old simulation, I keep the FOR, then > here it's stopped! Seeking for a solution! > There is one possible solution that I just thought of. Rather than using FOR as its own residue, create a formylated valine, thus eliminating the problem with the call to CA of the preceding residue. The .rtp entry: [ FVAL ] [ atoms ] CN CH1 0.380 0 ON O -0.380 0 N N -0.280 1 H H 0.280 1 CA CH1 0.000 2 CB CH1 0.000 3 CG1 CH3 0.000 4 CG2 CH3 0.000 5 C C 0.380 6 O O -0.380 6 [ bonds ] CN ON CN N N H N CA CA C C O CA CB CB CG1 CB CG2 [ impropers ] N CN CA H CN -CA N ON CA N C CB CB CG2 CG1 CA The .hdb entry: FVAL 1 1 1 H N CN CA Then add FVAL to residuetypes.dat as a protein residue. Processing the .pdb file you posted before (merging FOR and VAL into FVAL and adjusting names according to the .rtp entry above) works correctly. Disclaimer: this method "works" (i.e. produces a topology) but I do not necessarily endorse the use of the parameters shown. -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 * Only plain text messages are allowed! * 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 * Only plain text messages are allowed! * 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
