[gmx-users] Aromatic rings not plane after minimization

[Justin Lemkul]

On 4/15/14, 10:47 AM, Pierre THEVENET wrote:
> I am not using any rtp file. I thought the default parameters would be ok
> for standard amino acids.
> As I tried with different gromos force field, I suppose that I need to use
> a rtp file. But I don't understand
> what must be written in this file.
>

For pdb2gmx to work, it reads .rtp files that define what the residues are, how 
they're connected, and what parameters to assign, so you are, in fact, using 
.rtp files, whether you know it or not :)  Their content and format are 
explained in the manual.

The greater point is this - you don't have to change anything, nor should you. 
Improper dihedrals are used in the Gromos FF for aromatic and other planar 
systems.  Their presence does not guarantee absolute planarity over time (it's a 
harmonic function, after all, so the atoms can oscillate).  There's nothing to 
suggest that your observations are wrong or at all abnormal - aromatic rings can 
deform.  If it's a severe perturbation, as Mark alluded to before, it could be a 
consequence of other nasty things going on in the system that exert a greater 
force on the ring than the improper can restore.  That, however, is up to you to 
investigate and decide.

-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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