AMBER Archive (2003)

Subject: Re: AMBER: MM-PBSA question

From: Holger Gohlke (gohlke_at_bioinformatik.uni-frankfurt.de)
Date: Wed Dec 03 2003 - 12:58:23 CST

Giovanni schrieb:
>
> Dear all,
>
> I'd like to run a stability calculation - following the example
> provided with the sources - and I tried to generate snapshots from a
> trajectory. My complex is made of 48611 atoms, the first 8190 are
> protein atoms, 8191 - 8255 are ligand atoms and all the others are water
> and ions atoms.
> The MAKECRD of the input is like that:
>
> BOX YES
> NTOTAL 48611
> NSTART 1
> NSTOP 1000
> NFREQ 10
> #
> NUMBER_LIG_GROUPS 1
> LSTART 8191
> LSTOP 8255
> NUMBER_REC_GROUPS 1
> RSTART 1
> RSTOP 8190
>
> when I run the script I obtain a pipe interruption and the log file end
> like that:
>
> =>> Creating coordinates
> Executing makecrd
> Box info found: 79.094 89.637 84.508
> Something wrong with NGR 1 8190
>
> I fixed the bug 5.0 but I can't still run the script.

It's a good question - everything looks OK to me. Are you sure you
re-installed the fixed executable in the right place?

If it still doesn't work, you might want to send me your mm_pbsa.in file
as well as a short piece of your trajectory.

Best regards

Holger

>
> Please help me!
>
> TIA and Best Reguards,
>
> Giovanni
>
> --
> Dott. Giovanni Bottegoni
> Dep. of Medicinal Chemistry
> University of Bologna
>
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-- 
++++++++++++++++++++++++++++++++++++++++++++++++++
Dr. Holger Gohlke

J.W. Goethe-Universität
Fachbereich Biologie und Informatik
Institut für Mikrobiologie	
Marie-Curie-Str. 9              
60439 Frankfurt/Main            
Germany                         

Tel.:  (+49) 69-798-29503; Fax: (+49) 69-798-29826
Email: gohlke_at_bioinformatik.uni-frankfurt.de
URL:   http://www.rz.uni-frankfurt.de/~hgohlke
++++++++++++++++++++++++++++++++++++++++++++++++++

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