Re: [AMBER] atom clash and close contact after MD simulation in water

From: Vasantha Kumar <>
Date: Wed, 27 Jan 2016 17:40:14 +0100

Ciao Jacopo

Buona sera!!!
Grazie mille per la tua risposta.

I have a 8 mutation in my peptide, hence I have implemented the amber
ff99SB force-fields to handle these 8 residues.
The procedure that I have followed to implement the force-field is again
non standard protocol.
Yes NMR restraints are correct and amber reads it correctly. Off course I
will double check the volume of those peak again.
My NOESY spectra is bit crowded, I have to ease few noes which are in

Just to check I have run 20 ps SA in tip3pbox with restrains on where
starting structure were heated to 600K quickly and maintained at 600K for
few ps and cool back to 300K. In the last few steps I impose NMR restraints
and I vary the weight very slowly.

For the last point please correct me. After the MD I extract lower energy
structure which fall on the frames where temperature is 300K. Using this as
a reference structure I calculate the RMSD. From the stable RMSD region I
extract few models. It is true that these RMSD region falls in still
cooling steps. In these 10 models I am observing few clashes. You are
right, and what is the best way to extract good model if they dont have
stable rmsd ?

Grazie mille

2016-01-27 15:33 GMT+01:00 Carlos Simmerling <>:

> since you've combined several protocols this could arise from a few things.
> how do you determine there is a "clash"? visually, or by large vdw energies
> from the force field? if visual or anything other than the force field used
> for optimization, that might not be reliable. check your final MD data.
> also it could be that the force field and NMR restraints are in conflict,
> or that the structure is not well optimized by the annealing. non standard
> force field could be the cause too, but you don't describe the source or
> how it was tested. you need to go through the procedure step by step and
> check each of the possible causes.
> On Wed, Jan 27, 2016 at 8:50 AM, Vasantha Kumar <>
> wrote:
> > Dear AMBERist
> >
> > In a simulated annealing protocol I have refined the structure of small
> > peptide (chimeric) using nonstandard force-fields in water with NMR
> > restraints on. After the MD the pdb coordinates extracted from the stable
> > RMSD region shows clashes ans few bad contacts. Now I want fix it. Is it
> > common to observe clashes after md simulation, if yes how I can fix it is
> > there are some software tools available?
> >
> > thanks in advance...
> >
> > Vince
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> > AMBER mailing list
> >
> >
> >
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Received on Wed Jan 27 2016 - 09:00:03 PST
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