Hi Oliver,
you should not set the DIME value manually - the grid dimensions are set up
automatically based on your SCALE parameter. However, the SCALE parameter
is "Lattice spacing in no. of grids per Angstrom." so you probably want to
set it to 2, instead of 0.5.
If you still get the atoms out of the grid error message - could you send
me your input files? I'll take a look at this.
Thanks,
Robert
On Tue, Oct 13, 2009 at 10:36:27AM +0200, Oliver Kuhn wrote:
> 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 mm_pbsa_createinput.pm:
>
> ($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.
> regards
> Oliver Kuhn
>
>
>
>
>
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Received on Tue Oct 13 2009 - 08:00:02 PDT
