AMBER Archive (2002)

Subject: Re: amber7, gaff and minimization (fwd)

From: David A. Case (case_at_scripps.edu)
Date: Mon Aug 26 2002 - 20:35:26 CDT

On Mon, Aug 26, 2002, amber_at_heimdal.compchem.ucsf.edu wrote:
>
> I am trying to do minimization with explicit water for a protonated
> polymer with Cl- ions/ For the polymer I am using gaff.dat ff
> parameters. I have created appropiate lib file for the protonated polymer
> which xleap can read. With xleap added Cl- and TIP3P water. When I do
> minimization nothing happens in the sense that energy (or RMS) does not
> change after 100 steps of minimiation. Same thing continues for 3000 steps
> of conjugate gradient minimization.
> Can someone point out what is going wrong.

Please see my recent post about minimization tricks (on the archives of the
mailing reflector, within the last 2-3 weeks.) Turn SHAKE off and use a
large cutoff if you really need to get minimization. But the results you
showed might be fine if you are just using this as a prelude to doing
molecular dynamics.

..good luck...dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
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