AMBER Archive (2004)

Subject: Re: AMBER: xleap solvatebox problem

From: James W. Caldwell (jimc_at_stanford.edu)
Date: Wed Jun 09 2004 - 17:49:07 CDT

I tried your ACE example with Amber8 on a RedHat 8 system (note Leap
doesn't have any Fortran in it, it uses gcc only; are you using
gcc or the Portland C compiler?).

This looks normal to me:

Welcome to LEaP!
(no leaprc in search path)
> source leaprc.ff94
----- Source: /home/jimc/amber8/dat/leap/cmd/leaprc.ff94
----- Source of /home/jimc/amber8/dat/leap/cmd/leaprc.ff94 done
Log file: ./leap.log
Loading parameters: /home/jimc/amber8/dat/leap/parm/parm94.dat
Loading library: /home/jimc/amber8/dat/leap/lib/all_nucleic94.lib
Loading library: /home/jimc/amber8/dat/leap/lib/all_amino94.lib
Loading library: /home/jimc/amber8/dat/leap/lib/all_aminoct94.lib
Loading library: /home/jimc/amber8/dat/leap/lib/all_aminont94.lib
Loading library: /home/jimc/amber8/dat/leap/lib/ions94.lib
Loading library: /home/jimc/amber8/dat/leap/lib/solvents.lib
> a = ACE
> solvatebox a TIP3PBOX 10
  Solute vdw bounding box: 6.053 5.036 4.754
  Total bounding box for atom centers: 26.053 25.036 24.754
  Solvent unit box: 18.774 18.774 18.774
  Total vdw box size: 28.912 28.370 27.815 angstroms.
  Volume: 22814.792 A^3
  Total mass 8402.468 amu, Density 0.612 g/cc
  Added 464 residues.
>

On Wed, 2004-06-09 at 15:17, Shan, Jufang wrote:
> Hi,
>
> I had the same problem as the one raised by Tom before. http://structbio.vanderbilt.edu/archives/amber-archive/2004/1722.phtml
>
> When I solvate my system using xleap from Amber8 compiled using PGI 4.1 Fortran Complier on IBM Blade Servers runing RedHat 7.3, it gave me such info:
> > solvatebox h2 TIP3PBOX 8
> Solute vdw bounding box: 54.447 57.136 62.692
> Total bounding box for atom centers: 70.447 73.136 78.692
> Solvent unit box: 18.774 18.774 18.774
> Total vdw box size: 73.553 62.128 75.570 angstroms.
> Volume: 345334.587 A^3
> Total mass 304917.158 amu, Density 1.466 g/cc
> Added 14532 residues.
>
> And when I look at the structure, my protein is not been totally solvated, only part of it is in the rectangular waterbox. I checked the pdb file and found thre are ~20 waters in the same position.
>
> I followed Dr. Case's advice and solwated ACE:
>
> Welcome to LEaP!
> (no leaprc in search path)
> > source leaprc.ff94
> ----- Source: /nfs_exports/apps/pgi-apps/amber/dat/leap/cmd/leaprc.ff94
> ----- Source of /nfs_exports/apps/pgi-apps/amber/dat/leap/cmd/leaprc.ff94 done
> Log file: ./leap.log
> Loading parameters: /nfs_exports/apps/pgi-apps/amber/dat/leap/parm/parm94.dat
> Loading library: /nfs_exports/apps/pgi-apps/amber/dat/leap/lib/all_nucleic94.lib
> Loading library: /nfs_exports/apps/pgi-apps/amber/dat/leap/lib/all_amino94.lib
> Loading library: /nfs_exports/apps/pgi-apps/amber/dat/leap/lib/all_aminoct94.lib
> Loading library: /nfs_exports/apps/pgi-apps/amber/dat/leap/lib/all_aminont94.lib
> Loading library: /nfs_exports/apps/pgi-apps/amber/dat/leap/lib/ions94.lib
> Loading library: /nfs_exports/apps/pgi-apps/amber/dat/leap/lib/solvents.lib
> > solvatebox ACE TIP3PBOX 10
> Solute vdw bounding box: 6.053 5.036 4.754
> Total bounding box for atom centers: 26.053 25.036 24.754
> Solvent unit box: 18.774 18.774 18.774
> Total vdw box size: 28.912 22.002 22.520 angstroms.
> Volume: 14325.344 A^3
> Total mass 20220.964 amu, Density 2.344 g/cc
> Added 1120 residues.
> >
>
> I didn't experiece this problem using xleap from amber8 on SGI.
>
> Does anyone have any idea what is going on? Any comments will be appreciated!
>
> Thanks,
> Jufang
>
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-- 
James W. Caldwell					650-724-5322
Department of Chemistry
Clark Center, S2.2, Rm S294
Stanford University
Stanford, CA 94305-5447

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