AMBER Archive (2009)

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

From: Robert Konecny (rok_at_ucsd.edu)
Date: Tue Oct 13 2009 - 12:12:04 CDT

Hi Oliver,

see my in-line comments.

On Tue, Oct 13, 2009 at 05:17:06PM +0200, Oliver Kuhn wrote:
> Hi Robert,
>
> thanks for working on my problem.
> First of all, I know this scale parameter thing.
> I did it the right way all the time. Sorry.
> This is my input file:
>
> @GENERAL
> PREFIX snap
> PATH ./snapshots
> COMPLEX 1
> RECEPTOR 1
> LIGAND 1
> COMPT ./com.top
> RECPT ./rec.top
> LIGPT ./lig.top
> GC 0
> AS 0
> DC 0
> MM 1
> GB 0
> PB 1
> MS 0
> NM 0
>
>
> @PB
> PROC 3
> REFE 0
> INDI 1.0
> EXDI 80.0
> SCALE 2
> LINIT 1000
> PRBRAD 1.4
> ISTRNG 0.0
> RADIOPT 2
> DIME 161,161,129

Don't include the DIME parameter unless this is really what you want. iAPBS
should automatically figure out the optimal grid for the given SCALE
parameter.

>
> BCFL 2
> SRFM 1
> CHGM 1
> SWIN 0.3
> GAMMA 0.105
>

Don't include the following four parameters, they are not used by iAPBS. The
surface tension for the non-polar contribution is the GAMMA parameter (in
kJ/mol/A^2).

> CAVITY_SURFTEN 0.0072
> CAVITY_OFFSET 0.00
> SURFTEN 0.0072
> SURFOFF 0.00
>

Other than that it looks OK. Can you please rerun your calculation and let
me know if you still having problems.

All the best,

Robert

>
> @MM
> DIELC 1.0
>
>
> @MS
> PROBE 0.0
>
> (I would propably change the surften and surfoff to 0.00542 and 0.92, but thats not important at the moment)
>
> Anyway, I wanted to write you with the next error message I cannot understand.
> I got it working with setting dime manually and got:
> SURFTEN / SURFOFF values are not consistent across *.all.out files
> File header of the *.all.out files:
> ==> snap_com.all.out <==
> MM
> PB
> PB_SURFTEN 0.0072
> PB_SURFOFF 0.00
> 1
> BOND = 635.8445 ANGLE = 1611.2539 DIHED = 2167.6287
> VDWAALS = -1543.8684 EEL = -13389.5724 HBOND = 0.0000
> 1-4 VDW = 710.6519 1-4 EEL = 8866.5732 RESTRAINT = 0.0000
> corrected reaction field energy: -3487.712247
> ECAVITY = 251.7555
>
> ==> snap_lig.all.out <==
> MM
> PB
> PB_SURFTEN 0.0072
> PB_SURFOFF 0.00
> 1
> BOND = 18.0452 ANGLE = 42.3222 DIHED = 44.4127
> VDWAALS = -12.5880 EEL = -235.9055 HBOND = 0.0000
> 1-4 VDW = 30.9667 1-4 EEL = 209.1493 RESTRAINT = 0.0000
> corrected reaction field energy: -134.380176
> ECAVITY = 25.0821
>
> ==> snap_rec.all.out <==
> MM
> PB
> PB_SURFTEN 0.0072
> PB_SURFOFF 0.00
> 1
> BOND = 617.7993 ANGLE = 1568.9317 DIHED = 2123.2160
> VDWAALS = -1452.1121 EEL = -13096.1942 HBOND = 0.0000
> 1-4 VDW = 679.6852 1-4 EEL = 8657.4238 RESTRAINT = 0.0000
> corrected reaction field energy: -3538.290134
> ECAVITY = 261.8948
>
>
> regards
> Oliver
>
>
>
> > -----Ursprüngliche Nachricht-----
> > Von: "Robert Konecny" <rok_at_ucsd.edu>
> > Gesendet: 13.10.09 16:44:08
> > An: AMBER Mailing List <amber_at_ambermd.org>
> > Betreff: Re: [AMBER] iAPBS - how to set the right grid dimensions
>
>
> > 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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