[gmx-users] simulating hydrocarbons in water

[Adam Fraser]

Ah, okay thanks very much!  I thought-sure I had the most recent version,
but apparently not.  Still there's one quirk...

x2top -f HexA.gro -o HexA.top -r HexA.rtp -alldih
...This works to generate a topology file, but still, the program is
seg-faulting before writing out the residue type file (*.rtp).

I'm not yet sure if I can get by without the .rtp since hexadecane (C16)
won't likely be a recognized residue type.

Any ideas why this is seg-faulting or how I can get around the fact that
restype (C16) won't be recognized?

Thanks so much,
-Adam


On 10/10/07, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
>
> 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* <spoel at xray.bmc.uu.se
> > <mailto:spoel at xray.bmc.uu.se>> 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.
> >     spoel at xray.bmc.uu.se
> >     <mailto:spoel at xray.bmc.uu.se>    spoel at gromacs.org
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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.
> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://folding.bmc.uu.se
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