[gmx-users] Cytochrom C

[Robert Hamers]

   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 
> <mailto: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 <http://vt.edu> | (540) 231-9080
>     <tel:%28540%29%20231-9080>
>     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

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