Re: [AMBER] Minimization Failure

From: Taufik Al-Sarraj <>
Date: Wed, 24 Mar 2010 15:39:21 -0400

I just want to add what worked for me to close this thread properly.

My initial structures were 'very tense' so i decided to strip water and
ions and run minimization in vacuum for few hundred steps.

Then i added solvent and ions and ran a short minimization with SHAKE to
relax the water and ions while holding the rest of the system fixed.

now molecular dynamics is running happily.

Many Thanks,

Bill Ross wrote:
>> but can i do something about this, for example open the
>> prmtop file or the inpcrd file and 'somehow' find atom 4615 and change
>> its position?
> Technically you could do the math to figure out which numbers
> in the inpcrd to change (consider each atom has x, y, z coords).
> Or you could generate a pdb and look at it to actually understand
> what the problem is, posssibly fixing it and regenerating prmtop
> and inpcrd.
> What I'd be inclined to try is some 10K dynamics (with SHAKE)
> to see if that will get you over the problem. You might even
> go on to start your equilibration from there.
> Bill
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Received on Wed Mar 24 2010 - 13:00:02 PDT
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