Re: amber7, gaff and minimization (fwd)

From: David A. Case <>
Date: Mon 26 Aug 2002 18:35:26 -0700

On Mon, Aug 26, 2002, 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

David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
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Received on Mon Aug 26 2002 - 18:35:26 PDT
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