[gmx-users] dihedral doubt

[Andres Ortega Guerrero]

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 

Thanks again


Andres Ortega

> 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 
> following:
> 
> 1. In [dihedraltypes] in ffbonded.itp
> 2. In the .top in a [dihedraltypes] directive declared before the first 
> [moleculetype]
> 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
> 
> -- 
> ==================================================
> 
> 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
> http://mackerell.umaryland.edu/~jalemkul
> 
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