[gmx-users] Cytochrom C

Dariush Mohammadyani d.mohammadyani at gmail.com
Fri Jan 6 19:18:38 CET 2012


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
>>
>> ========================================
>>
>> --
>> gmx-users mailing list    gmx-users at 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-request at 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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120106/cc6ef734/attachment.html>


More information about the gromacs.org_gmx-users mailing list