[gmx-users] Aromatic rings not plane after minimization

[Pierre THEVENET]

Ok, thank all of you for your help. I will try to figure out which greater
force cause this perturbation.


--------------------------

Pierre THEVENET
Ph.D. Student
INSERM - MTi
Ecole Doctorale B3MI
Université Paris Diderot - Paris 7



2014-04-15 16:56 GMT+02:00 Justin Lemkul <jalemkul at vt.edu>:

>
>
> 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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