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

From: Vasantha Kumar <>
Date: Wed, 27 Jan 2016 17:48:44 +0100

Dear Carlos

Good evening...

I load final structures to chimera, there with the option find clashes and
contact (based on vDW) I found these problem. For the moment I have used
default values to
check the clashes and contact.

When I implemented the force-field I used non standard protocol where I am
sure geometry of the block is not 100% optimized. Adding charge I used
AM1-BCC method instead of RESP. Its true force-filed also causing problem.

I will give a try to see my MD data

thanks a lot fro your suggestion..

Have a nice day!!!

2016-01-27 17:40 GMT+01:00 Vasantha Kumar <>:

> 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
> overlaps.
> 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
> Vasantha
> 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
>> > _______________________________________________
>> > AMBER mailing list
>> >
>> >
>> >
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Received on Wed Jan 27 2016 - 09:00:05 PST
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