MM_PBSA Errors

From: (wrong string) ón Garduño-Juárez <>
Date: Tue 11 Feb 2003 18:16:00 -0600

Dear Amber users:

I am using the AMBER tool known as MM_PBSA in order to perform a comparison
between the energies between different orientations of some inclusion
complexes. For some of them I have been able to run MM_PBSA to the end,
thus obtaining the corresponding energies. However, for a few of them my
run MM_PBSA crashes with the following error message:

ERROR: MSMS program output is missing
check snapshot # 251 in file
correct and rerun mm_pbsa_statistics<in>out

The snapshot number varies according to my sampling scheme
The file try_GB_new_?????.out sometimes is that of the host, sometimes is
that of the guest

I have tried to get around this problem by increasing or decreasing NFREQ,
NSTART or NSTOP parameters in the mm_pbsa script. My trajectory file comes
from AMBER v5 and MM_PBSA comes from AMBER v6. As far as I can see mm_pbsa
has worked in other cases but I wonder why I am getting this weird behavior
and how I can fix it.

I will appreciate any comments, hints and fixes. Much obliged.

Ramón Garduño
Received on Tue Feb 11 2003 - 16:16:00 PST
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