[gmx-users] Creating top-file for molecules not included in the forcefield

[Justin A. Lemkul]

Sascha Rehm wrote:
> Dear users,
> 
> quite some weeks ago I asked you for help in creating some organic 
> solvents with the OPLS force field.
> I read chapter 5 and started to build the molecule structures and also 
> the corresponding itp-files. Since all of the needed atom types were 
> found in the OPLS forcefield, this worked fine.
> 
> One question I couldn't figure out was how I get the top-file.
> I wanted to convert my solvent molecule with pdb2gmx into a .gro file, 
> add a box und fill it with more of the solvent molecules, to get a pure 
> solvent system.
> But pdb2gmx doesn't know the molecule (of course, because it's not a 
> residue known to the forcefield). Normally I would add a "#include 
> solvent.itp" - line in the topology file of a system, so that gromacs 
> can deal with the unknown molecule (like I do when solvating a protein 
> with water). But in my case there is no topology-file, so I cannot 
> include an .itp-file
> 
> Question: Can someone tell me, how I can connect my molecule to my 
> .itp-file to build up a pure-solvent-system ? How do I continue after 
> building a structure and itp-file?
> 

The main difference between a .top and a .itp file is that a .top is a 
system-level topology, containing all molecule definitions for all species in 
the simulation.  At the top, the force field is specified, i.e.:

#include "ffoplsaa.itp"

This line that is not present in an .itp, which just contains a single molecule 
definition.

After you've defined your molecule, include [ system ] and [ molecules ] 
directives, and you've defined a .top file.

If these concepts are unfamiliar, perhaps some tutorial material using a simple 
protein (processed by pdb2gmx) will give you some clues as to structure and 
organization.

-Justin

> I couldn't figure it out in the manual and didn't find anything in the 
> mailing list :-/
> 
> Thanks a lot,
> Sascha
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-- 
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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