AMBER Archive (2004)

Subject: AMBER: Problems using mm_pbsa.perl

From: Daniel Wetzler (danielwetzler_at_appleinfo.de)
Date: Fri Nov 05 2004 - 10:28:15 CST


Hallo,

I'm trying to repeat the task of calculating the protein-stability using
the mm_pbsa.pl skript.
To perform my task I just copied the configuration file of the
example and adapted it to my files.

At the first step I created Snapshots of my mdcrd-file using an adapted
configuration-file.

My problem is now, that the .crd files created by the script do not
comply to my
.top (topology-files).
I can't perform the calculation of the stability because I get the error :

FATAL: NATOM mismatch in coord and topology files

If I want to calculate pdb-files out of my .crd-files I also get an error :

daw_at_cu16 mmpbsa > ambpdb -p sgdphe_protein.top_alt <
sgdphe_protein_com.crd.1 > sgdphe_protein_com.pdb.1
| New format PARM file being parsed.
| Version = 1.000 Date = 10/25/04 Time = 18:43:24

 ATOMS DO NOT MATCH BETWEEN PARM AND MIN FILES 13613 3907

Does nayone know why my .top files don't comply my .crd-files ?

Hope anyone can help.

Best wishes,

Daniel
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