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.ucsd.edu>
> Gesendet: 13.10.09 16:44:08
> An: AMBER Mailing List <amber.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
> >
> >
> >
> >
> >
> > ______________________________________________________
> > GRATIS für alle WEB.DE-Nutzer: Die maxdome Movie-FLAT!
> > Jetzt freischalten unter http://movieflat.web.de
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________________________
Neu: WEB.DE DSL bis 50.000 kBit/s und 200,- Euro Startguthaben!
http://produkte.web.de/go/02/
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Oct 13 2009 - 08:30:02 PDT
