AMBER Archive (2009)

Subject: [AMBER] iAPBS - how to set the right grid dimensions

From: Oliver Kuhn (
Date: Tue Oct 13 2009 - 03:36:27 CDT

Dear iAPBS users and developers,

I got this error message, that my grid is to small and atoms are out of the mesh.
I have found this outcommented line in the

($dimex, $dimey, $dimez) = split(/,/,$r_del->{"DIME"});

Then I had to add:
print OUT " dime = ${dimex}, ${dimey}, ${dimez},\n";

and I set
DIME 161,129,129
in my mmpbsa input file.

I do not really think, that's what I'm supposed to do.

The question is: How do I know what dimensions to set?
or Why do I have to set dimensions manually?
I would have to start one pdb2pqr run on one snapshot to get suggested dimensions,
in my case:
dime 161 129 129
cglen 101.7654 70.7540 73.9126
fglen 79.8620 61.6200 63.4780
Would I still need SCALE 0.5 when using explicit cglen and fglen?
I think, I could use: DIME with SCALE or DIME with CGLEN and FGLEN.

If I set DIME manually, how could I then set different dimensions for my protein and ligand which is much smaller?

Help on this is appreciated.
Oliver Kuhn

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