[gmx-users] Creating topology for a small organic molecule

Justin A. Lemkul jalemkul at vt.edu
Sun Oct 25 22:48:44 CET 2009

Gunnar Widtfeldt Reginsson wrote:
> Hi. 
> I need to create a topology file for a small organic molecule that is to 
> interact non- covalently with a DNA duplex. I want to use the amber99 
> force field.
> I saw on this mailing list that you can use acpypi with antichamber to 
> create a topology for amber force fields. I got the amber10 tools and 
> installed but I couldn't find any more information on how to get the 
> antichamber package to work. I am finding this all very complicated 
> since I am not an expert in the unix language, so if anyone knows about 
> a good beginners tutorial on how to install antichamber and acpypi could 
> you please let me know were to find it.

Since antechamber is part of the AMBER package, I would suggest reading the 
AMBER manual.

The acpypi documentation is online:


> Another question is, how difficult is it to create the topology for the 
> molecule by hand for the amber99 force field. Could someone please get 
> me started on that, if it would be easier. The molecule is a derivative 
> of cytosine.

Parameterization is an expert topic.  Please see here:



> I am using GROMACS 4 on Mac OS 10.5
> Thanks.
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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