Hello everyone! I have been trying to calculate the binding free energy
between protein and calcium ion using mm_pbsa.pl. I've successfully got
snapshot_com.crd.*, snapshot_rec.crd.* and snapshot_lig.crd.*, but failed
when tried to calculate binding energy from these snapshots. The log file
indicates that this program failed when it got to snapshot_lig.crd.1. The
following is part of log file including the failure point. I also noticed
that the PDB file generated for ligand (calcium here) has coordinates
(0.000, 0.000, 0.000) for calcium, which is not true because
snapshot_lig.crd.1 gave another set of coordinates. Could anyone tell me why
this happened? Is it a particular problem for metal ligand? Thanks a lot!
Calc contrib for ./snapshot_rec.crd.199
Calc MM/GB/SAS
Generate PDB
Center PDB
Calc PBSA
Generate PQR
Calc MS
Calc contrib for ./snapshot_rec.crd.200
Calc MM/GB/SAS
Generate PDB
Center PDB
Calc PBSA
Generate PQR
Calc MS
Calc contrib for ./snapshot_lig.crd.1
Calc MM/GB/SAS
Generate PDB
Center PDB
Calc PBSA
Xue
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Received on Wed Sep 01 2010 - 13:30:06 PDT
