Much appreciated, works beautifully!<br><br><div><span class="gmail_quote">On 10/10/07, <b class="gmail_sendername">TJ Piggot</b> <<a href="mailto:t.piggot@bristol.ac.uk">t.piggot@bristol.ac.uk</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;">
Just as a note editconf will covert a pdb to a gro file<br><br>Tom<br><br>--On Wednesday, October 10, 2007 09:47:03 -0400 Adam Fraser<br><<a href="mailto:adam.n.fraser@gmail.com">adam.n.fraser@gmail.com</a>> wrote:<br>
<br>> Yes I tried this and it doesn't work for me. I get:<br>><br>><br>> Fatal error:<br>> Library file ffG53a6.n2t not found in current dir nor in default<br>> directories.<br>> (You can set the directories to search with the GMXLIB path variable)
<br>><br>> Also, doesn't x2top take in a gro file? (not a pdb) I wrote a script<br>> that converts pdb to gro, and I still get the above error.<br>><br>> -Adam<br>><br>><br>> On 10/10/07, David van der Spoel <
<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>> wrote:<br>><br>> 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>> _______________________________________________
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><br>><br><br><br><br>----------------------<br>TJ Piggot<br><a href="mailto:t.piggot@bristol.ac.uk">t.piggot@bristol.ac.uk</a><br>University of Bristol, UK.<br><br>_______________________________________________<br>
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