[gmx-users] Building simple alcohol topologies

[Mark Abraham]

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.

Mark