Gromos96 53A6 has it. On 2012-01-06 01:18:38PM -0500, Dariush Mohammadyani wrote: > I tried charmm27 too. > > Error: > Residue 'ACE' not found in residue topology database > > I tried all forcefield in the list provided by "pdb2gmx", but non of them > works. > > Dariush > > > On Thu, Jan 5, 2012 at 1:42 PM, Robert Hamers <rjham...@wisc.edu> wrote: > > > HEME is in the charmm27 force field. > > bob h. > > > > > > > > > > On 1/5/2012 12:00 PM, Dariush Mohammadyani wrote: > > > > Yes, I have PDB file (1HRC.pdb). However, when I try to use "pdb2gmx" I > > get this error: > > > > Residue 'HEM' not found in residue topology database > > > > and HEM is Iron ion inside this protein. I do not know which forcefield is > > proper to use. I also tried MARTINI force field according their website; I > > used martinize.py script; Again I got error. > > > > Regards, > > Dariush > > > > > > > > > > On Thu, Jan 5, 2012 at 11:51 AM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > >> > >> > >> Dariush Mohammadyani wrote: > >> > >>> > >>> Hi all, > >>> > >>> Has anybody made initial configuration for Cytochrom C? Can it be shared > >>> with me? > >>> > >>> > >> There are several in the PDB. > >> > >> -Justin > >> > >> -- > >> ======================================== > >> > >> Justin A. Lemkul > >> Ph.D. Candidate > >> ICTAS Doctoral Scholar > >> MILES-IGERT Trainee > >> 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 > >> > > > > > > > > > > > > > > > > -- > > Robert J. Hamers > > Wisconsin Distinguished Professor > > Univ. of Wisconsin-Madison > > 1101 University Avenue > > Madison, WI 53706 > > Ph: 608-262-6371 > > Web: http://hamers.chem.wisc.edu > > > > > > > -- > Kind Regards, > Dariush Mohammadyani > Department of Structural Biology > University of Pittsburgh School of Medicine > Biomedical Science Tower 3 > 3501 Fifth Avenue > Pittsburgh, PA 15261 > USA
> -- > 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 -- ================================================================== Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | ================================================================== -- 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
