Btw if you want a CHARMM27 version you should be able to parameterize it from the existing atomtypes like (not verified) (adapted from ALA):
[ ACE ] [ atoms ] CH3 CT3 -0.27 0 HH31 HA 0.09 1 HH32 HA 0.09 2 HH33 HA 0.09 3 C C 0.51 4 O O -0.51 5 [ bonds ] CH3 H1 CH3 H2 CH3 H3 CH3 C C O Surprisingly, an .hdb entry for ACE exists so you don't need to create one. On 2012-01-06 12:23:49PM -0600, Peter C. Lai wrote: > 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 -- ================================================================== 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
