Dear Rosa, here goes my little contribution to try to help you: <a href="http://acpypi.googlecode.com">http://acpypi.googlecode.com</a>.<div><br></div><div>For me, no doubt that antechamber is the best tool for getting the topological information about small molecules (pls, read the wikis in ACPYPI pages to know more).</div>
<div><br></div><div>The module to generate OPLS/AA is still experimental but if you take information from MKTOP (which I intend to add to ACPYPI eventually) then you can get something good enough, specially if you do your homework and read the papers related to this matter.</div>
<div><br></div><div>Cheers,</div><div>Alan<br><br><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">Subject: [gmx-users] oplsaa parametrization<br>
<br>
Dear Users<br>
I m trying to simulate a structure (not a protein) which is not<br>
parametrized in oplsaa FF. I created the structure using PRODRG and<br>
included the results of *.itp from PRODRG to ffoplsaa.rtp file and tried<br>
to use available oplss_xxx for my atom type near to those ones already<br>
exists in *.atp. I also optimized my structure at RHF/6-31G* level and<br>
calculated the charge using resp. Then updated ffoplsaa.rtp using this<br>
calculated charge. By refering to the mailing list it seems that I need<br>
to modify bn.itp and nob.itp file as well (?!). I m just wonder if<br>
anybody use PRODRG how he/she parametrized FF. As I m new in GROMACS and<br>
any tutorial or procedure to follow will help me so much. Thank you in<br>
advance for any ideas or comments.<br>
<br>
Also when I use pdb2gmx, I have this warning; all CONECT records are<br>
ignored. However when I proceed with energy minization in vacuum the<br>
program doesnt complain and it can produce *.tpr file.<br>
<br>
Regards<br>
Rosa<br>
<br></blockquote></div>-- <br>Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate<br>Department of Biochemistry, University of Cambridge.<br>80 Tennis Court Road, Cambridge CB2 1GA, UK.<br>>><a href="http://www.bio.cam.ac.uk/~awd28">http://www.bio.cam.ac.uk/~awd28</a><<<br>
</div>