you could try to write your top files in the working directory and use pdb2gmx -ff option. By default, gromacs first searches in the working directory.<br><br>amit<br><br><div class="gmail_quote">On Sat, Nov 14, 2009 at 9:05 AM, Jiang Zhu <span dir="ltr"><<a href="mailto:zhujiang2005@gmail.com">zhujiang2005@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;">Dear all,<br><br> I have been a GROMACS user for some time but this is my first time to handle a modified residue with an additional chemical group linked to the side chain. I do not have the permission to change/add the topology file in the system directory where GROMACS package is located. I am wondering if there is any other way to force pdbgmx to read residue topo file from specified location or other tricks I can play. Thanks for your help!<br>
<br>Best regards,<br><font color="#888888">Jiang<br>
</font><br>--<br>
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