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On 14/04/2011 5:59 PM, hui sun wrote:
<blockquote cite="mid:76069.60633.qm@web15306.mail.cnb.yahoo.com"
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<div><font size="3">Dear all,</font></div>
<div><font size="3"> </font></div>
<div><font size="3">I am having the troubles to obtain the
topology file for Cytochrome C. When I used the
Gromos96 53a6 force filed in the GROMACS
4.0.7 software package, the topology file is produced,
but there is lack of some force field parameters, such
as the bonds from Cys 14 and Cys 17 to the porphyrin
ring and to hold the ligands (Met 80 and His 18) bound
to the heme iron, in this file. When I used the
Gromos96 53a6 force filed in the GROMACS
4.5.1 software package, there's a fatal error: Residue
'HEM' not found in residue topology database. I have
checked the rtp file, in which there is the "HEME"
residue. </font></div>
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<br>
"HEM" will not always be considered the same as "HEME" by a computer
algorithm... If they're meant to match, name them the same thing in
each place.<br>
<br>
Mark<br>
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