AMBER Archive (2009)

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

From: Oliver Kuhn (oak.amber_at_web.de)
Date: Tue Oct 13 2009 - 10:17:06 CDT


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

BCFL 2
SRFM 1
CHGM 1
SWIN 0.3
GAMMA 0.105

CAVITY_SURFTEN 0.0072
CAVITY_OFFSET 0.00
SURFTEN 0.0072
SURFOFF 0.00

@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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