[gmx-users] Aromatic rings not plane after minimization

[Justin Lemkul]

On 4/15/14, 10:03 AM, Pierre THEVENET wrote:
>>
>> I do not know how you do the magic connected with the topology
>> derivation, but please make sure that all needed dihedrals were
>> introduced. x2top, for instance, does not write dihedrals.
>>
>>
> To produce the topology, I use pdb2gmx, I thought it would write the proper
> dihedrals. Am I wrong?
>

pdb2gmx will write the correct terms.  In fact, g_x2top does, as well, if you 
specify the correct options.  Missing dihedrals are possible with g_x2top if one 
uses default options, but that also depends on the force field being used.

-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

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