AMBER Archive (2004)

Subject: RE: AMBER: xleap solvatebox problem

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Wed Jun 09 2004 - 17:48:12 CDT

Dear Shan,

A couple of questions, first of all does your installation of Amber8 on the
IBM Blade servers pass all of the tests? If not can you please let me know
what the errors are. Also, if you use tleap do you get the same problem?

Secondly could you please send me the input files that you are using for
xleap (a pdb?) and a list of the commands you entered in xleap so that I can
try and see if I can reproduce this.

Also, the IBM Blades, do you know what CPUs they have and/or their model
numbers?

All the best
Ross

/\
\/
|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk/ | PGP Key available on request |

  

> -----Original Message-----
> From: owner-amber_at_scripps.edu
> [mailto:owner-amber_at_scripps.edu] On Behalf Of Shan, Jufang
> Sent: 09 June 2004 15:18
> To: amber_at_scripps.edu
> Subject: AMBER: xleap solvatebox problem
>
> 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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