I am using ffG43a1 forcefield. its .rtp file contains topology of Heme but Met SD and FE bond is not there.<div>Shahid Nayeem<br><br><div class="gmail_quote">On Thu, Nov 25, 2010 at 5:11 AM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div class="im"><br>
<br>
Erik Marklund wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
shahid nayeem skrev 2010-11-24 18.02:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear all<br>
I am trying MD of cyt C containing heme. I am able to generate bonds with specbond.dat by pdb2gmx. After using editconf and genbox, when I tried grompp I got error about unrecognized bonds/angles. I made bond with MET SD and FE of Heme. As earlier suggested on this list I wrote to get parameter for these bonds but I couldnt get it. If someone on this mailing list can help me I will be grateful. Cyt C is very widely modelled protein with Gomacs in literature hence I expect to get some help from the forum.<br>
shahid nayeem<br>
</blockquote>
A long time ago I simulated CytC with one of the gromos force fields. It worked right out of the box. What forcefield are you using?<br>
<br>
</blockquote>
<br></div>
The same problem is frequently reported. The inter-residue bonds and angles are not assigned in pdb2gmx, nor are they present in the force field, IIRC. Hence the fatal errors. Perhaps something has changed since "a long time ago," but I am sure problems exist in recent versions.<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> | (540) 231-9080<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>
========================================<div><div></div><div class="h5"><br>
-- <br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
</div></div></blockquote></div><br></div>