AMBER Archive (2005)

Subject: AMBER: leap issues on a powerbook

From: justin litchfield (litch_at_stanford.edu)
Date: Sun Jun 12 2005 - 18:21:02 CDT

i installed AMBER on my powerbook using the g95 fortran compiler, and
everything seems to work, but i've found one thing that's pretty
odd. i'm trying to make a protein-ligand complex and paramaterized
the ligand with antechamber, and the frcmod doesn't put in any
parameters. when i run this script in tleap using the attached input
files, that does something like this:
read ligand
read pore
combine ligand and pore into complex
write pdb of ligand, pore and complex
write amber input files for ligand, pore and complex

it does everything fine up until writing amber input for ligand,
pore, and then in writing the complex it hangs at
Marking per-residue atom chain types.

this will hang indefinitely (presumably, i left it for a couple hours
with it going at full CPU usage.

if i run the same script with same input files on my G5 it works fine.

attached are all the files i run with the following command
tleap -f makeamberins
also, the relevant leap.log

thanks,

justin





  • application/applefile attachment: leap.log

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