Ah, okay thanks very much! I thought-sure I had the most recent version, but apparently not. Still there's one quirk...<br><br>x2top -f HexA.gro -o HexA.top -r HexA.rtp -alldih<br>
...This works to generate a topology file, but still, the program is seg-faulting before writing out the residue type file (*.rtp).<br><br>I'm not yet sure if I can get by without the .rtp since hexadecane (C16) won't likely be a recognized residue type.
<br><br>Any ideas why this is seg-faulting or how I can get around the fact that restype (C16) won't be recognized?<br><br>Thanks so much,<br>-Adam<br><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>> Yes I tried this and it doesn't work for me. I get:<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><br>did you use 3.3.2 ? The default and only supported FF there is OPLS. For<br>GROMOS variants you can try the prodrg webserver.<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>> On 10/10/07, * David van der Spoel* <<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a><br>> <mailto:
<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
<br>> like this<br>> > one.<br>> ><br>> > I've built topologies for hexadecane compatible with NAMD, so I<br>> 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
<br>> 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>
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