[gmx-users] Building simple alcohol topologies

[David van der Spoel]

Mark Abraham wrote:
> Jussi Lehtola wrote:
>> Hi,
>>
>>
>> I've been trying to find all-atom topologies and atom coordinates for
>> 1-alcohols (from ethanol to 1-decanol, possibly also n-alcohols) to be
>> used in MD simulations for electronic structure calculations. However I
>> haven't found any, also I haven't found any guides on how to construct
>> such files.
> 
> Your first order of business is to identify a suitable force field 
> http://wiki.gromacs.org/index.php/Force_Fields - probably any of them 
> will do for n-alcohols. Then you would like some automated tool to build 
> your topologies. The pdb2gmx utility in GROMACS is not suited to your 
> task. Perhaps the AMBER LeAP utility is closer to your needs - but it 
> does require the use of AMBER force fields, which will be OK for you. 
> You will also need to generate your initial structures with atoms 
> suitably named - LeAP will also help there.
> 
>> 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.

> 
> Mark
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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