AMBER Archive (2002)

Subject: Re: why is mm_pbsa broken ? (fwd)

From: Holger Gohlke (gohlke_at_scripps.edu)
Date: Tue Aug 27 2002 - 12:12:17 CDT

Hi,

from what I see from your data files, although you might have got
numbers for the single molecules but not for the "binding" calculation,
there were already problems with the "stability" calculations. Please,
do not only check the XXX_statistics.out file but also the XXX_{com,
rec, lig}.all.out files.

1. Not for all snapshots of com and rec, SAS area was calculated by
molsurf. I had to set "NUM_NEIGHBOR" in molsurf.c to "200", to avoid
"MAX_NEIGHBOR exceeded" messages. Your protein is rather big, so
sometimes there are more than 100 neighbors for each atom, as was
assumed for the default value.

2. To use the Jayaram et al. MBG model as indicated by IGB=4 in your
mm_pbsa.in, you also have to use the proper radii. For this, please do
"set default PBradii mgbjsb" in (x)leap before saving your prmtop files.
This might be the reason why you got "nan" values for EGB in the
XXX_{com, rec, lig}.all.out.

3. Finally, your electrostatic solvation free energies as calculated by
delphi are all zero. You might want to comment the line "unlink
$delphiout;" in the subroutine calc_PB in mm_pbsa.pl to obtain delphi
log files.

I hope this helps - best regards

Holger

> Dear all,
>
> I have a question about the perl of mm_pbsa. I use it for free enery calculations following as
> the examples in the tutorial. It works very well for calculating the energy of complex (protein
> + ligand), but a "binding" calculation (deltaG for A + B --AB), the program is broken. And
> "mm_pbsa.out" is cutoff at the line "calc delta", three files of "com.all.out + rec.all.out+
> lig.all.out " exist well, but I couldn't find the important output file " _statistics.out".
> the ligand is calculated with antechamber and the force field is used as gaff.dat. by the
> way, if I only calculate the energy of ligand, the rate is very very slow, why?
>
> Any suggestions would be greatly appreciated.
>
> Thanks in advance.
>
> Jiang
>
> 　　　　　　　　　　　　　　Yongjun Jiang
> 　　　　　　　　　　　　　　yjjiang_at_mail.shcnc.ac.cn
> 　　　　　　　　　　　　　　　　　2002-08-22 

-- 
+++++++++++++++++++++++++++++++++++++++++++++
Dr. Holger Gohlke
Dept. of Molecular Biology, TPC15
The Scripps Research Institute
10550 N. Torrey Pines Rd.
La Jolla CA 92037  USA
phone: +1-858-784-9788
fax:   +1-858-784-8896
email: gohlke_at_scripps.edu
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