[gmx-users] Building simple alcohol topologies

[David van der Spoel]

Jussi Lehtola wrote:
>> Mark Abraham wrote:
>>>> If anyone could give me a few pointers on how and where to obtain these,
>>>> I'd appreciate it a lot.
> 
>> Or you type them in manually. Not a lot of work.
>> Or you use x2top, which for alcohols and OPLS works reasonably well.
> 
> 
> OK, how can I obtain the coordinates, then? PDB doesn't seem to contain
> alcohols. I found some compounds from HIC-Ub, but for instance heptanol
> is missing.
molden
prodrg
jmol

google is your friend

-- 
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