[gmx-users] butane-parameters

Justin A. Lemkul jalemkul at vt.edu
Thu Sep 17 20:49:51 CEST 2009

rversace at ccny.cuny.edu wrote:
> Hi Everybody:
> I am trying to perform a MD simulation of n-butane. But I cannot find the gromacs paramaters for it. In the 2005 paper from Lange about Flooding in GROMACS (J.Comp.Chem 21:1693.2006), the authors performed this simulation before using the ffgmx united atom force field. But I cannot find the butane topology and parameters inside that forcefield. 
> When I use pdb2gmx on my butane.pdb I get the following message:
> -------------------------------------------------------
> Program pdb2gmx, VERSION 4.0.4
> Source code file: resall.c, line: 426
> Fatal error:
> Residue 'BUT' not found in residue topology database
> -------------------------------------------------------
> Does anybody know where can it be or maybe it has another residue name in the rtp file?  

The .rtp files generally only contain protein (and sometimes nucleic acid) 
residues.  Generating a united-atom (or even all-atom) topology for butane by 
hand should be a trivial exercise.  A Gromos topology would have four atoms, 
three bonds, three angles, and one dihedral.

Refer to Chapter 5 in the manual for topology organization and format.


> 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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