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

From: Jacopo Sgrignani <>
Date: Wed, 27 Jan 2016 15:03:05 +0100

Dear Vasantha
what do you mean for nonstandard FF?
In my opinion observing clashes and bad contacts after MD simulation is not

In theory you should remove clashes and contacts minimising the structure
the more important question is why you observe these clashes and contacts.

Are you sure that the NMR restraints are correct? or that Amber correctly
reads your file?

Another hypothesis is that you have problems with the SA procedure but, if
you decrease the temperature
before saving the conformation where you see clashes, you should not
observe clashes.


2016-01-27 14:50 GMT+01:00 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 - 06:30:03 PST
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