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
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