Thank you mark for your suggestion. can i use x2top to generate topology for oplsaa force field by using (all atom) .gro file from PRODRG?.Is it worth using it.<br><br>Regards<br>Vinoth<br><br><div class="gmail_quote">On Tue, Oct 5, 2010 at 11:30 AM, Mark Abraham <span dir="ltr"><<a href="mailto:mark.abraham@anu.edu.au">mark.abraham@anu.edu.au</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">Pre-supposing the suitability of only one tool is pretty limiting - and that's before you consider the weaknesses of PRODRG even for its target forcefields.<br>
<br>For decane, writing the topology by hand is feasible. There's at most 3 atom types and only 32 atoms, after all. Otherwise, consider <a href="http://www.gromacs.org/index.php?title=Download_%26_Installation/Related_Software/MKTOP" target="_blank">http://www.gromacs.org/index.php?title=Download_%26_Installation/Related_Software/MKTOP</a><br>
<br>Mark<div><div></div><div class="h5"><br>----- Original Message -----<br>From: vinothkumar mohanakrishnan <<a href="mailto:kmvinoth@gmail.com" target="_blank">kmvinoth@gmail.com</a>><br>Date: Tuesday, October 5, 2010 16:43<br>
Subject: [gmx-users] Reg: Prodrg topology<br>To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br><br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>Hi all<br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>I want to generate a topology file for say decane from prodrg for oplsaa force field. is it possible?. i get a topology file from prodrg for gromos96.1 force field and i am able to process it further. when i use the topology file generated for gromos96.1(from prodrg) for oplsaa i get the error (during grompp) as atomtype CH3 not found ( as expected, i know why it happens). hence my question is how to use oplsaa for decane molecule?<br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>Regards<br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>Vinoth<br></div></div> > -- <br>> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
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