For a single ion, the coordinate really doesn't matter. The energy
will be a constant throughput the trajectory.
As for the failure on the single ion calculation, it's probably due to
the complaint in PBSA that fillratio (=2) is set to be too small if you
are using one of the earlier Amber distributions. Do a search on the
list to find out how to add "fillratio =4" in the PBSA input, which is
automatically generated by the perl script.
All the best,
Ray
==========================================
Ray Luo, Ph.D.
Associate Professor in Computational
Biochemistry and Molecular Biophysics
Dept of Molecular Biology and Biochemistry
Dept of Biomedical Engineering
University of California, Irvine, CA 92697-3900
Email: rluo.uci.edu Phones: (949) 824-9528, 9562
Web: http://rayl0.bio.uci.edu/rayl/
==========================================
On 9/1/2010 1:14 PM, xue wang wrote:
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Sep 01 2010 - 15:00:04 PDT
