Yes I tried this and it doesn't work for me. I get:<br><div style="margin-left: 40px;"><br>Fatal error:<br>Library file ffG53a6.n2t not found in current dir nor in default directories.<br>(You can set the directories to search with the GMXLIB path variable)
<br><br></div>Also, doesn't x2top take in a gro file? (not a pdb) I wrote a script that converts pdb to gro, and I still get the above error.<br><br>-Adam<br><br><div><span class="gmail_quote">On 10/10/07, <b class="gmail_sendername">
David van der Spoel</b> <<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Adam Fraser wrote:<br>> Hello,<br>><br>> I'm very new to Gromacs, and I am interested in simulating the<br>> interactions of 2 hexadecane (C16H34) molecules in water (SPC/E<br>> specificall). I've spent some time experimenting with tutorials in
<br>> Gromacs, but I've found little help in non-protein simulations like this<br>> one.<br>><br>> I've built topologies for hexadecane compatible with NAMD, so I figure I<br>> should be able to do the same in Gromacs but I'm fuzzy on how to go
<br>> about doing so (what files to edit). I was also hoping to get some<br>> input on which forcefield would be best for this sort of system.<br>><br>> I'd greatly appreciate it if someone could give me some pointers on how
<br>> to get started here.<br>><br>> Thanks very much,<br>> Adam<br>><br>if you have a pdb file you can run x2top (3.3.2 only).<br><br>><br>> ------------------------------------------------------------------------
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</a><br><br><br>--<br>David van der Spoel, Ph.D.<br>Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.<br>Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.<br><a href="mailto:spoel@xray.bmc.uu.se">
spoel@xray.bmc.uu.se</a> <a href="mailto:spoel@gromacs.org">spoel@gromacs.org</a> <a href="http://folding.bmc.uu.se">http://folding.bmc.uu.se</a><br>_______________________________________________<br>gmx-users mailing list
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