[gmx-users] Structure Breaking during minimization

[Justin Lemkul]

On 10/25/16 10:02 AM, Apramita Chand wrote:
> Dear All,
> I'm trying to incorporate charges and topology obtained from ATB server for
> taurine into GROMOS53a6 ff by copying into my local working directory and
> adding information in the .rtp file. All other commands work smoothly but
> after energy minimzation, except for the NH3+ group, all the other bonds
> are broken and individual atoms are just scattered randomly.
> What could be the reason?

Without seeing your full .rtp entry, it's impossible to say.  Your topology 
defines bonds between the atoms as expected, right?

> I have taken the pdb file from ATB server and generated the .itp file too.
> From there, I have taken the charges and the bonded parameters like
> bonds,angles I'm assigning the gromos types which are sometimes different
> from what has been given in the .itp file. Is it wrong? Should I add new
> bonded parameters too in the ffbonded.itp?
>

grompp complains if there are missing parameters.  If you didn't get a fatal 
error, the parameters you need are already present.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
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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