AMBER Archive (2009)

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

From: Robert Konecny (rok_at_ucsd.edu)
Date: Wed Oct 14 2009 - 08:21:07 CDT

Hi Oliver,

can you send me (off list) your input files (with just few snapshots) -
I'll take a look at this.

Best,

Robert

On Wed, Oct 14, 2009 at 03:16:28PM +0200, Oliver Kuhn wrote:
> Hi Robert,
> I'm still running with the dime manually set just to get one run through.
> I removed
> > > CAVITY_SURFTEN 0.0072
> > > CAVITY_OFFSET 0.00
> > > SURFTEN 0.0072
> > > SURFOFF 0.00
> from my input file and get
>
> Use of uninitialized value $mm_pbsa_statistics::gammaP in multiplication (*) at /home/kuhn/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1391.
> Use of uninitialized value $mm_pbsa_statistics::betaP in addition (+) at /home/kuhn/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1391.
>
> Do I have to set something like
> GAMMAP 0.00542
> BETAP 0.92
>
> regards
> Oliver
>
>
> > -----Ursprüngliche Nachricht-----
> > Von: "Robert Konecny" <rok_at_ucsd.edu>
> > Gesendet: 13.10.09 19:14:33
> > An: AMBER Mailing List <amber_at_ambermd.org>
> > Betreff: Re: [AMBER] iAPBS - how to set the right grid dimensions
>
>
> > 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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