<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Dear Sarada,<div><br></div><div>You need to paramterize the Cysteinyl ligand manually. There are a variety of references in the literature that provide reasonable energies. Below is a pretty good reference.</div><div><br></div><div>Best wishes,</div><div>Art</div><div><br></div><div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 36px; text-indent: -36px; font: normal normal normal 12px/normal Helvetica; ">1.<span class="Apple-tab-span" style="white-space:pre"> </span>Oda, A., Yamaotsu, N., and Hirono, S. (2005) New AMBER force field parameters of heme iron for cytochrome P450s determined by quantum chemical calculations of simplified models, <i>J. Comput. Chem.</i> <i>26</i>, 818-826.</div><div style="text-indent: -36px;"><br></div><div style="text-indent: -36px;"><br></div><div><div>On Dec 9, 2008, at 10:59 PM, <a href="mailto:saradas@ncbs.res.in">saradas@ncbs.res.in</a> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Hello,<br>I am working with the simulation of cytochromeP450. There is a bond<br>between the S of cystine and FE of HEME. During the grompp step I get<br>warnings that there is no default bonds/angles/dihedrals all pertaining to<br>the cystine-heme bond. In the archives it was mentioned that these values<br>must be taken from ffG**bon.itp and included in the topology file. However<br>in the ffG**bon.itp file, the bonds/angles mentioned seem to be between S<br>of CYS and the carbon atom of HEME. For eg,<br><br>; bond-, angle- and dihedraltypes for specbonds:<br>[ bondtypes ]<br>S S 2 gb_33<br>NR FE 2 gb_32<br>; cystine - heme link (is CR1-S, use CH2-S):<br>S CR1 2 gb_30<br><br>Should not the cystine - heme link have FE insteadof CR1? I understand<br>that I am missing some crucial point here. Kindly help.<br>Thanks.<br>Sarada<br>Graduate student,<br>NCBS,<br>Bangalore<br><br><br><br><br><br>_______________________________________________<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at http://www.gromacs.org/search before posting!<br>Please don't post (un)subscribe requests to the list. Use the<br>www interface or send it to gmx-users-request@gromacs.org.<br>Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br></div></blockquote></div><br></div></body></html>