From: Holger Gohlke <>
Date: Thu, 20 Nov 2003 13:36:30 +0100

Chenglong Li wrote:
> Dear AMBER users,
> In MM_PB/GB/SA analysis, I have problems with both un-reduced and
> reduced complex approaches:
> 1) With the whole system, the igb=4 minimizations are too slow because
> of
> the large size of the protein.

I don't quite see where the minimizations come into play? The basic idea
of MM_PB/GBSA is to generate an ensemble of structures and then to use
these structures (w/o minimization) for calculation of the MM, PB/GB,
and SA part. In the case of estimating vibrational entropies by normal
mode analysis (the only place where I would use a minimization), a
reduced number of snapshots can be used without too much affecting the
precision of the results.

Best regards


> If I change to cut=16 from without
> cutoff,
> it converges much faster so I can use much fewer maxcyc.
> But I don't know if it's a good choice because a) the energies are
> different;
> b) MM may be off quite a bit. Even if deltaG may not got affacted much
> due to
> cancelling-out, still may be larger than it should be.
> 2) If I cut a reduced system out centered around the ligand, the new
> complex
> contains a lot of short pieces of individual peptide strands. The
> re-creaction of
> the receptor and complex prmtops introduces some new H in the
> N-terminals and
> new OXT in the C-terminals. These new atoms of course are not in the
> original
> snapshots taken out of MD trajectories. It looks that you cannot get a
> prmtop
> with leap without these new atoms because leap would complain the large
> distances between the terminal atoms. I wonder how to get a workable
> reduced
> complex model.
> Ant solution is welcome.
> Thanks,
> Chenglong Li
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to
> To unsubscribe, send "unsubscribe amber" to

Dr. Holger Gohlke
J.W. Goethe-Universität
Fachbereich Biologie und Informatik
Institut für Mikrobiologie	
Marie-Curie-Str. 9              
60439 Frankfurt/Main            
Tel.:  (+49) 69-798-29503; Fax: (+49) 69-798-29826
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Thu Nov 20 2003 - 12:53:00 PST
Custom Search