AMBER Archive (2009)

Subject: [AMBER] trouble using iAPBS

From: Oliver Kuhn (
Date: Mon Sep 28 2009 - 07:08:27 CDT

Hi amber users,

I want to use iAPBS within MMPBSA and I am facing two problems:

1. Using RADIOPT=0, I get the following error:

many of these atoms out of mesh
Vpmg_fillco: Atom #74 at (48.701, 40.490, 33.014) is off the mesh (ignoring):
Vpmg_fillco: xmin = 32.6135, xmax = 48.6135
Vpmg_fillco: ymin = 32.1415, ymax = 48.1415
Vpmg_fillco: zmin = 24.2735, zmax = 40.2735
SURFTEN / SURFOFF values are not consistent across *.all.out files

tension and offset values are printed in the head of the outfiles and are all 0.0072 and 0, so it looks as if they were consistent.
I think, there is something missleading with this error message.
I used the configuration from the amber manual.

2. I want to use RADIOPT=2 and have no idea where to set the modifications to build pdbs and pqrs.
First idea was, to write pdbs and pqrs from any of the crd-snapshots, but I am quite sure, that's not what is meant in the manual.
The manual proposes to create lig.pqr, rec.pqr and com.pqr from lig.pdb, rec.pdb and com.pdb.
The mechanism of the mmpbsa-script is, to work sequentially on all com-files, rec-files and then lig-files.
Can anyone give me hints for the right code modifications?

thanx in advance

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