Also, have a read at <a href="http://acpype.googlecode.com">acpype.googlecode.com</a>.<div><br></div><div>Alan<br><br><div class="gmail_quote">On 21 September 2010 06:36, manoj singh <span dir="ltr"><<a href="mailto:mks.amber@gmail.com">mks.amber@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">First, you have to develop parameter for your molecule withing Amber. Then you have to create .prmtop and .inpcrd files for your molecule, and than you can convert the Amber topology to Gromacs topology. You will need AmberTools and a script called <a href="http://amb2gmx.pl" target="_blank">amb2gmx.pl</a>.<br>
<br>Following links would be helpful for you<br><br><a href="http://ambermd.org/#AmberTools" target="_blank">http://ambermd.org/#AmberTools</a><br><br><a href="http://ambermd.org/antechamber/efz.html" target="_blank">http://ambermd.org/antechamber/efz.html</a><br>
<br><span><span><span><cite><a href="http://ffamber.cnsm.csulb.edu/" target="_blank">ffamber.cnsm.csulb.edu/</a><b>amb2gmx</b>.<b>pl</b></cite></span></span></span><div><div></div><div class="h5"><br>
<br><div class="gmail_quote">On Tue, Sep 21, 2010 at 12:51 AM, vivek sharma <span dir="ltr"><<a href="mailto:viveksharma.iitb@gmail.com" target="_blank">viveksharma.iitb@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left:1px solid rgb(204, 204, 204);margin:0pt 0pt 0pt 0.8ex;padding-left:1ex">
Hi There,<br>
I am trying to run molecular dynamics on a drug-enzyme complex using<br>
amber force field. I have done it earlier using gromos FF using<br>
drug-enzyme tutorial, I dont know if the parameter set (.mdp file)<br>
will be same or different while using AMBER FF.<br>
Any insight/comments into the matter may be of help if somebody has<br>
tried using AMBER FF for docked complex in GROMACS.<br>
<br>
Thanks in advance.<br>
<br>
regards,<br>
Vivek<br>
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