AMBER Archive (2009)

Subject: [AMBER] MM-PBSA problem

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Dear all,

I am trying to run a MM-PBSA simulation (receptor + ligand). I prepared the ligand using the

"BASIC WORKSHOP HANDS ON TUTORIAL 4" to calculate partial charges and missing parameters. Then i prepared the jobs using the Advanced Tutorial A3. I run the jobs without problem. When i run the binding_energy.mmpbsa script, the output results shows something very strange. The numbers for complex and receptor were fine, but for the ligand i got extremely big numbers as shown in the attached files. Can someone imagine why this happened? Has anyone else had the same problem? Please tell me which other files I must attached to help you find a solution.

 Best Regards,

Dr George Lamprinidis

School of Pharmacy

University of Athens

Greece

• application/octet-stream attachment: snapshot_statistics.out

• application/octet-stream attachment: snapshot_statistics.out.snap

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• Previous message: Aust, Susanne: "[AMBER] analysis of QM/MM - LCOD"
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