AMBER Archive (2008)

Subject: Re: AMBER: Protein rotating out of box

From: Lars Skjærven (lars.skjarven_at_biomed.uib.no)
Date: Wed Apr 02 2008 - 16:01:54 CDT

I just tried it with sleap in amber10 as well. same result. maybe not
surprising. anyway worth mentioning. hmm... can the size of the solute
be a potential problem?

By the way, sleap does not like the closeness parameter:

lars_at_lars-desktop:~/tmp/solvate_oct_test$ sleap
[gtkleap]$ source leaprc.ff03
using file /usr/local/amber10/dat/leap/cmd/leaprc.ff03
using file /usr/local/amber10/dat/leap/gleap/parm99.dat
using file /usr/local/amber10/dat/leap/parm/frcmod.ff03
using file /usr/local/amber10/dat/leap/lib/ions94.lib
using file /usr/local/amber10/dat/leap/lib/solvents.lib
using file /usr/local/amber10/dat/leap/lib/all_nucleic94.lib
using file /usr/local/amber10/dat/leap/lib/all_aminoct94.lib
using file /usr/local/amber10/dat/leap/lib/all_aminont94.lib
using file /usr/local/amber10/dat/leap/lib/all_amino03.lib
[gtkleap]$ source leaprc.gaff
using file /usr/local/amber10/dat/leap/cmd/leaprc.gaff
using file /usr/local/amber10/dat/leap/gleap/gaff.dat
[gtkleap]$ set default fastbld on
[gtkleap]$ mol = loadpdb protein.pdb
[gtkleap]$ solvatebox mol TIP3PBOX 12.0 0.78
Error: wrong number of arguments
[gtkleap]$ solvateBox mol TIP3PBOX 12.0
box size : 174.180 177.935 172.886
[gtkleap]$

Thanks.

LarsS

On Wed, Apr 2, 2008 at 9:17 PM, Lars Skjærven
<lars.skjarven_at_biomed.uib.no> wrote:
> thanks again for feedback.
>
> Both vmd and xleap is used for visualization. tLeap adds a total of
> 40k waters, which is ~50k less than when i solvate with 'solvatebox
> 5Å'. Thus, I doubt visualization is the reason for this.
>
> Amber9 with the newest bugfixes is used. I've tried this on three
> independent machines (SGI altix, and two linux boxes). Portland group
> compilers has not been used on any of the installations.
>
> When I reduce the size of the same protein by 50%, it solvates as expected.
>
> LarsS
>
>
>
> On Wed, Apr 2, 2008 at 7:35 PM, Qiang Li <hi_liqiang_at_yahoo.com> wrote:
> >
> > Hi,
> > I meet the same problem too. I was following the tutorial on AMBER website,
> > and I never manage to put the whole DNA into the box. I am using amber 8,
> > Portland Group compiler, and AMD opteron. David A. Case just told me that
> > the PGC should be the reason. Are you using PGC too?
> >
> > --Qiuting Hong
> >
> >
> > ----- Original Message ----
> > From: Thomas Cheatham III <tec3_at_utah.edu>
> > To: amber_at_scripps.edu
> > Sent: Wednesday, April 2, 2008 9:54:46 AM
> > Subject: Re: AMBER: Protein rotating out of box
> >
> >
> > > Thanks for your comments. I guess the solvateoct is the way to go
> > > here. However, after I solvate using the command:
> > > 'solvateoct mol TIP3PBOX 15.0 0.78' parts of the solute is outside the
> > > box. Hmm.. Does not the buffer argument, in this case 15.0Å, specify
> > > the distance between the wall of the box and the closest atom? Or is
> > > it the distance to the walls in the cubic box, and then it shawes off
> > > the corners no matter if the solute is in the way? I have to make the
> > > buffer as high as 33Å to get the solute entirely inside the box.
> > --------------------------
> >
> > ________________________________
> > You rock. That's why Blockbuster's offering you one month of Blockbuster
> > Total Access, No Cost.
>
>
>
> --
>
>
> mvh Lars Skjærven
> Institutt for Biomedisin
> Universitetet i Bergen
> 

-- 
mvh Lars Skjærven
Institutt for Biomedisin
Universitetet i Bergen
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