AMBER Archive (2003)

Subject: AMBER: MM-PBSA question

From: Giovanni (gio_at_scfarm.unibo.it)
Date: Wed Dec 03 2003 - 12:10:10 CST


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.

Please help me!

TIA and Best Reguards,

Giovanni

-- 
Dott. Giovanni Bottegoni
Dep. of Medicinal Chemistry
University of Bologna

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