AMBER: solvatebox problem in the antechamber tutorial

From: Heiko Meyer <>
Date: Wed, 09 Mar 2005 17:29:00 +0100

Dear Amber Users
Iīm having a problem running the antechamber-tutorial:
Everything works fine until generating the solvate box.
I tried it several times but I canīt find the failure.
I always got nearly 5 times more water then expectet.
Also the density is much to high.
Analysing the generated PDB-File I find that allways
several water molecules lie exactly on top of each other.
AMD Athlon XP
Fedora Core 2

Thank You in advance

Here is the XLEaP - Protocol:

Welcome to LEaP!
Sourcing: /home/chemsim/progs/linux/amber8/dat/leap/cmd/leaprc.ff99
Log file: ./leap.log
Loading parameters:
Loading library:
Loading library:
Loading library:
Loading library:
Loading library: /home/chemsim/progs/linux/amber8/dat/leap/lib/ions94.lib
Loading library: /home/chemsim/progs/linux/amber8/dat/leap/lib/solvents.lib
> source leaprc.gaff
----- Source: /home/chemsim/progs/linux/amber8/dat/leap/cmd/leaprc.gaff
----- Source of
/home/chemsim/progs/linux/amber8/dat/leap/cmd/leaprc.gaff done
Log file: ./leap.log
Loading parameters: /home/chemsim/progs/linux/amber8/dat/leap/parm/gaff.dat
> loadamberprep sustiva.prepin
Loading Prep file: ./sustiva.prepin
> loadamberparams sustiva.frcmod
Loading parameters: ./sustiva.frcmod
Reading force field mod type file (frcmod)
> check SUS
Checking 'SUS'....
Checking parameters for unit 'SUS'.
Checking for bond parameters.
Checking for angle parameters.
Unit is OK.
> solvateoct SUS TIP3PBOX 10
Scaling up box by a factor of 1.288419 to meet diagonal cut criterion
  Solute vdw bounding box: 12.038 10.678 8.029
  Total bounding box for atom centers: 37.807 37.807 37.807
      (box expansion for 'iso' is 16.0%)
  Solvent unit box: 18.774 18.774 18.774
  Volume: 29220.916 A^3 (oct)
  Total mass 62452.856 amu, Density 3.549 g/cc
  Added 3449 residues.

Heiko Meyer
Fraunhofer-Institute for Algorithms and Scientific Computing (SCAI)
Schloss Birlinghoven
D-53754 Sankt Augustin, Germany
Phone: 	+49 - (0)2241 - 14 2574
Fax:   	+49 - (0)2241 - 14 2181
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Wed Mar 09 2005 - 16:53:01 PST
Custom Search