[gmx-users] impropers in Gromacs and acepype tool

Justin Lemkul jalemkul at vt.edu
Thu Mar 6 23:26:57 CET 2014

On 3/6/14, 5:16 PM, Chetan Mahajan wrote:
> Hi
> I just wanted to check the order of atoms in a improper in gromacs input
> file *.top. According to urea example on page 137 ( section 5.7)of manual
> 4.6.4, order of i,j,k,l atoms in improper always starts with central atom,
> whereas that in a *.top file generated with acepype lists i,j,k,l order for
> improper in formate ion as H O C O. Central atom at third position. Is this
> right or bug in the tool acepype?

It's right.  The example in the manual is for Gromos force fields.  You should 
look at the actual .rtp files for the AMBER parameter set you're trying to use. 
  Suffice it to say that different atom orders are supported, because the 
Gromacs machinery (specifically pdb2gmx) knows how to deal with lots of stuff 
based on bonded geometry.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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