AMBER Archive (2009)

Subject: Re: [AMBER] trouble using iAPBS

From: Robert Konecny (rok_at_ucsd.edu)
Date: Mon Sep 28 2009 - 09:20:31 CDT

Hi Oliver,

On Mon, Sep 28, 2009 at 02:08:27PM +0200, Oliver Kuhn wrote:
> 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

that's exactly what it says - your grid is too small and some atoms are off
the mesh. You need to increase size of the grid.

> 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?

Yes, you just need a single set of .pqr files (for lig, rec and com). iAPBS
uses only charge and radius values from the .pqr files and these remain
same for all snapshots. The actual coordinates are taken from individual
crd snapshots.

Best,

Robert

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