AMBER Archive (2004)

Subject: AMBER: xleap solvatebox problem

From: Shan, Jufang (Jufang.Shan_at_stjude.org)
Date: Wed Jun 09 2004 - 17:17:59 CDT

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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