AMBER Archive (2006)

Subject: Re: AMBER: mm_pbsa_statistical.pl

From: William Wei (william.wei_at_utoronto.ca)
Date: Wed Aug 30 2006 - 16:11:51 CDT

Hi all,

Thanks In Hee Park for your information. I tried to run
"mm_pbsa_statistical.pl 2 0 O_statistics.in O_statistics.out > sta.out". I
got the following message:
use of uninitialized value at ./amber7/src/mm_pbsa_statistics.pm line 1235
use of uninitialized value at ./amber7/src/mm_pbsa_statistics.pm line 1235
use of uninitialized value at ./amber7/src/mm_pbsa_statistics.pm line 1203
use of uninitialized value at ./amber7/src/mm_pbsa_statistics.pm line 1203
      No data for 0+0 MS SURF 0

The O_statistics,in was generated from mm_pbsa. I have the GB/PB outputs
for com, rec, and lig from mm_pbsa. I checked these three files, except
some trajectories do not have "surface area", the other output seems to be
okay.

Could anybody give some suggestions?

Thanks,
 William

----- Original Message -----
From: "In Hee Park" <ipark_at_chemistry.ohio-state.edu>
To: "William Wei" <william.wei_at_utoronto.ca>
Sent: Wednesday, August 30, 2006 4:21 PM
Subject: Re: AMBER: mm_pbsa_statistical.pl

> HI,
>
> What I referred to is just AMBER mailing list, please see
> http://amber.ch.ic.ac.uk/archive/200601/0012.html
>
> For more details, I'll also try to take a look at the
> mm_pbsa_statistis.pm module.
>
> ___________________
> In Hee Park
>
>
> [2006-08-30.Wed.9:13am] William Wei wrote `Re: AMBER:
mm_pbsa_statistical.pl'
>
> Dear In Hee Park,
>
> Thank you very much for your help. For the first digit, does it related
to
> IGB in the GB section? Do you have any reference for that?
>
> Thanks again,
> William
>
> ----- Original Message -----
> From: "In Hee Park" <ipark_at_chemistry.ohio-state.edu>
> To: "William Wei" <william.wei_at_utoronto.ca>
> Sent: Tuesday, August 29, 2006 5:29 PM
> Subject: Re: AMBER: mm_pbsa_statistical.pl
>
>
> > I've just had same trouble, since no detailed instruction for this.
But
> > I figured out how to use it finally.
> >
> > What you need is just produced "filename_{com,rec,lig}.all.out" files
> > and "filename_statistics.in" file. Check that "filename_statistics.in"
> > has all three lines:
> > filename_com.all.out
> > filename_rec.all.out
> > filename_lig.all.out
> >
> > Then just type following:
> > (This is specific case for using 1T and no decomposition.)
> > mm_pbsa_statistics.pl 1 0 filename_statistics.in
filename_statistics.out
> > ***
> > Note that the two digits can be changed depending on your own need,
for
> > example:
> > first digit : 1 (1T), 2 (3T)
> > second digit : 0 (no decomposition), 2 (do decomposition)
> > ___________________
> > In Hee Park
> >
> >
> > [2006-08-29.Tue.5:02pm] William Wei wrote `AMBER:
mm_pbsa_statistical.pl'
> >
> > Dear all,
> >
> > I was using mm_pbsa to calculate the deltaG. By some reason it
stopped
> at
> > statistical accounting. Because it took a long time to finish the
free
> > energy for my snapshots. I have the output for Com. Rec. and Lig.
from
> > mmpbsa. What is the command for "mm_pbsa_statistical"?
> >
> > usage: mm_pbsa_statistics.pl <calc delta ? 0..1> <input file>
<output
> > file>
> >
> > what is the first parameter "calc delta ? 0..1". If I have 100
> snapshots
> > for Com, rec. and lig. what is my input?
> >
> > Anybody used that? Thanks in advance,
> > William
> >
>
> -----------------------------------------------------------------------
> > The AMBER Mail Reflector
> > To post, send mail to amber_at_scripps.edu
> > To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
> >
> >
>
>
>

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu