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.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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Received on Fri Nov 05 2004 - 16:53:00 PST
