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

From: Carlos Simmerling <>
Date: Wed, 27 Jan 2016 09:33:36 -0500

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 <>

> 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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Received on Wed Jan 27 2016 - 07:00:03 PST
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