[gmx-users] dihedral doubt
Andres Ortega Guerrero
og_andres15 at hotmail.com
Sun Mar 2 00:54:12 CET 2014
Thanks Justin for your help, i will modify the i j k l of the dihedral in my topology to correspond to the bonded.itp
> Date: Sat, 1 Mar 2014 18:39:04 -0500
> From: jalemkul at vt.edu
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] dihedral doubt
> On 3/1/14, 6:27 PM, Andres Ortega Guerrero wrote:
> > Thanks Justin for the advice and help,
> > So i have to add in the bonded.itp
> > O_2 C_2 CT OH with the parameters? or in the topology file (molecule) , y define the dihedral like OH CT C_2 O_2 ???
> Either way. The dihedral's parameters either need to exist in any one of the
> 1. In [dihedraltypes] in ffbonded.itp
> 2. In the .top in a [dihedraltypes] directive declared before the first
> 3. Explicitly printed on the line with the corresponding atom numbers in the
> [dihedrals] directive
> If any of those is true, it will work.
> 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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