[gmx-users] butane-parameters

[Justin A. Lemkul]

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.

-Justin

> 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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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