Adam Fraser wrote:
Yes I tried this and it doesn't work for me. I get:
Fatal error:
Library file ffG53a6.n2t not found in current dir nor in default
directories.
(You can set the directories to search with the GMXLIB path variable)
did you use 3.3.2 ? The default and only supported FF there is OPLS. For
GROMOS variants you can try the prodrg webserver.
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.
-Adam
On 10/10/07, * David van der Spoel* <[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>> wrote:
Adam Fraser wrote:
> Hello,
>
> I'm very new to Gromacs, and I am interested in simulating the
> interactions of 2 hexadecane (C16H34) molecules in water (SPC/E
> specificall). I've spent some time experimenting with tutorials in
> Gromacs, but I've found little help in non-protein simulations
like this
> one.
>
> I've built topologies for hexadecane compatible with NAMD, so I
figure I
> should be able to do the same in Gromacs but I'm fuzzy on how to go
> about doing so (what files to edit). I was also hoping to get some
> input on which forcefield would be best for this sort of system.
>
> I'd greatly appreciate it if someone could give me some pointers
on how
> to get started here.
>
> Thanks very much,
> Adam
>
if you have a pdb file you can run x2top (3.3.2 only).
>
>
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--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]> [EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]> http://folding.bmc.uu.se
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David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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