<div dir="ltr">I tried charmm27 too. <br><br>Error:<br>Residue 'ACE' not found in residue topology database<br><br>I tried all forcefield in the list provided by "pdb2gmx", but non of them works.<br><br>Dariush<br>
<br><br><div class="gmail_quote">On Thu, Jan 5, 2012 at 1:42 PM, Robert Hamers <span dir="ltr"><<a href="mailto:rjhamers@wisc.edu">rjhamers@wisc.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
HEME is in the charmm27 force field. <br>
bob h.<div><div class="h5"><br>
<br>
<br>
<br>
On 1/5/2012 12:00 PM, Dariush Mohammadyani wrote:
<blockquote 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 href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div><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>
</blockquote>
<br>
</div>
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>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | <a href="tel:%28540%29%20231-9080" value="+15402319080" target="_blank">(540) 231-9080</a><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================
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</div>
</blockquote>
</div>
<br>
<br clear="all">
<br>
<br>
</div>
<br>
<fieldset></fieldset>
<br>
</blockquote>
<br>
</div></div><span class="HOEnZb"><font color="#888888"><pre cols="72">--
Robert J. Hamers
Wisconsin Distinguished Professor
Univ. of Wisconsin-Madison
1101 University Avenue
Madison, WI 53706
Ph: <a href="tel:608-262-6371" value="+16082626371" target="_blank">608-262-6371</a>
Web: <a href="http://hamers.chem.wisc.edu" target="_blank">http://hamers.chem.wisc.edu</a></pre>
</font></span></div>
</blockquote></div><br><br clear="all"><br>-- <br><div dir="ltr"><div>Kind Regards,<br>Dariush Mohammadyani<br>Department of Structural
Biology<br>University of Pittsburgh School of Medicine<br>Biomedical Science
Tower 3<br>3501 Fifth Avenue<br>Pittsburgh, PA 15261<br>USA</div></div><br>
</div>