[gmx-users] Cytochrom C

[Peter C. Lai]

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 <rjhamers at 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 <jalemkul at 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
> >>
> >> ========================================
> >>
> >> --
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> >>
> >
> >
> >
> >
> >
> >
> >
> > --
> > 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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