[gmx-users] dihedral doubt

[Justin Lemkul]

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

==================================================