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HEME is in the charmm27 force field. <br>
bob h.<br>
<br>
<br>
<br>
On 1/5/2012 12:00 PM, Dariush Mohammadyani wrote:
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cite="mid:CAAk3nxcDxmOAD0WHaGCctUAxLskNnVFM50WixSuEm=HytQqi0g@mail.gmail.com"
type="cite">
<div dir="ltr">Yes, I have PDB file (1HRC.pdb). However, when I
try to use "pdb2gmx" I get this error:<br>
<br>
Residue 'HEM' not found in residue topology database<br>
<br>
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.<br>
<br>
Regards,<br>
Dariush<br>
<br>
<br>
<br>
<br>
<div class="gmail_quote">On Thu, Jan 5, 2012 at 11:51 AM, Justin
A. Lemkul <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span>
wrote:<br>
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<div class="im"><br>
<br>
Dariush Mohammadyani wrote:<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt
0.8ex;border-left:1px solid
rgb(204,204,204);padding-left:1ex">
<br>
Hi all,<br>
<br>
Has anybody made initial configuration for Cytochrom C?
Can it be shared with me?<br>
<br>
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There are several in the PDB.<br>
<br>
-Justin<br>
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
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target="_blank">vt.edu</a> | <a moz-do-not-send="true"
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========================================
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<pre class="moz-signature" cols="72">--
Robert J. Hamers
Wisconsin Distinguished Professor
Univ. of Wisconsin-Madison
1101 University Avenue
Madison, WI 53706
Ph: 608-262-6371
Web: <a class="moz-txt-link-freetext" href="http://hamers.chem.wisc.edu">http://hamers.chem.wisc.edu</a></pre>
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