Dear amber users,
I have been trying to reproduce the procedure used in Amber tutorial A9 - "Thermodynamic Integration using soft core potentials" with a transformation of myristate to palmitate which involves the removal of a proton from the myristate ion then changing myristate to palmite which involves the addition of an ethyl group.
However the soft core step bombs (step 2) due to a coordinate error. I have compared the 2 pdb files produced by the second leap run and they appear to be well superposed with the exception of the soft core atoms of course. I have attached the pdb files and my script file and the leap scripts and the minimization log files. I am obviously doing something wrong but cannot trace the problem. Any ideas?
Regards,
Tony Pemberton
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- application/octet-stream attachment: step2.sh
- application/octet-stream attachment: leap1.in
- application/octet-stream attachment: leap2.in
Received on Tue Dec 08 2009 - 08:30:02 PST
