AMBER Archive (2005)

Subject: Re: AMBER: big fluctuation in MM-PBSA/GA

From: Eric Hu (eric.y.hu_at_gmail.com)
Date: Fri Apr 15 2005 - 16:42:45 CDT

On 4/15/05, Xin Hu <hux_at_mail.rockefeller.edu> wrote:
> > On 4/15/05, Xin Hu <hux_at_mail.rockefeller.edu> wrote:
> >> >
> >> > A snapshot was taken every 2ps for binding energy calculation
> >> > (according to Tutorial_03). Here is the statistics.out.
> >> >
> >>
> >> Hi Eric,
> >> I am a newer of MM_PBSA. What's the tutorial_03?
> >
> > /amber8/src/mm_pbsa/Examples/03_MMPBSA_Binding/
> >
>
> Hi Eric,
> Thanks for your help.
> I tested these examples before. One question about the input parameter in
> /amber8/src/mm_pbsa/Examples/mm_pbsa.in, should I just use all the defacult
> parameters for my own project, such as the GB parameters, the MAXCYC=10000
> and DRMS=0.0001 for NM, the CHARGE (my_amber94_delphi.crg) and SIZE
> (my_parse_delphi.siz) for the PB delphi (PROC=1), etc? I am not sure whether
> these parameters are specifically used by Dr. Gohlke for the Ras_Raf work,
> or they are generally optimized and applicable to other works?
Well, this is a hard question and varies case to case. It not only
depends on your system but also your experience. Basically, you can
use most of the default parameters and play with them until you are
satisfied.

Eric
>
> Thanks,
>
>
> Xin
>
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