AMBER Archive (2009)

Subject: [AMBER] myristate to palmitate transformation

• Previous message: Carlos Simmerling: "Re: Re: [AMBER] ptraj usage for clustering of protein ensembles manual or tutorial"
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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

• application/octet-stream attachment: plm_check.pdb

• application/octet-stream attachment: step2.sh

• application/octet-stream attachment: plm_min_v1_l1.out

• application/octet-stream attachment: myr_check.pdb

• application/octet-stream attachment: myr_min_v0_l1.out

• application/octet-stream attachment: leap1.in

• application/octet-stream attachment: leap2.in

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• Previous message: Carlos Simmerling: "Re: Re: [AMBER] ptraj usage for clustering of protein ensembles manual or tutorial"
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