<div>Dear all,</div> <div> </div> <div>I have made MD simulations of fullerene derivatives using Tripos FF, for short simulation time. I would like to extend these simulations using faster program GROMACS.</div> <div> </div> <div>Is there any way to convert Tripos FF and structure files to gromacs *.itp, and *.pdb files, respectively? (I tried to convert pdb file to gmx *.itp and *.pdb files using PRODRG, but it failed). <BR></div> <div>Best Wishes,</div> <div> </div> <div> </div> <div>Serdar Durdagi</div> <div> </div> <div> </div> <div> </div> <div><BR><B><I>Mark Abraham <Mark.Abraham@anu.edu.au></I></B> schrieb:</div> <BLOCKQUOTE class=replbq style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #1010ff 2px solid">Luis Javier Alvarez wrote:<BR>> Dear Mark:<BR>> Thanks for your response to my mail on the initial configuration for <BR>> gromacs. Since in your reply you
implicitly posed some questions I am <BR>> writing directly to you to ask you something in the hope that it shall <BR>> not bother you.<BR><BR>Please leave gromacs-related correspondence on the list. That way it's <BR>archived for others to find later.<BR><BR>> You mentioned that there is the question of wether or not we have access <BR>> to the right tools to set up the initial configuration for gromacs to <BR>> generate the topology file. In fact we do not have anything specialised. <BR>> We are using what we can get from the internet and if necessary we write <BR>> our own programs. So the question is: what are these right tools?<BR><BR>Various force fields have tools that are suited for topology-generation, <BR>like Antechamber or PRODRG or x2top or pdb2gmx, and your choice of force <BR>field will be connected with the availability of such tools and the <BR>nature of your simulation
system.<BR><BR>Mark<BR>_______________________________________________<BR>gmx-users mailing list firstname.lastname@example.org<BR>http://www.gromacs.org/mailman/listinfo/gmx-users<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 email@example.com.<BR>Can't post? Read http://www.gromacs.org/mailing_lists/users.php<BR></BLOCKQUOTE><BR><p>
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