Hello all,
Here is the similar problem with lteap installed in Opteron compiled with
PGI. I find that the water molecules are far away from the UNIT. Any
suggestions to fix this problem will be highly appreciated.
> solvateoct UNIT TIP3PBOX 5
Scaling up box by a factor of 3.375128 to meet diagonal cut criterion
Solute vdw bounding box: 63.748 64.032 53.122
Total bounding box for atom centers: 97.784 97.784 97.784
(box expansion for 'iso' is 12.9%)
Solvent unit box: 18.774 18.774 18.774
Volume: 481974.749 A^3 (oct)
Total mass 759950.659 amu, Density 2.618 g/cc
Added 40140 residues.
Sincerely,
Jiten
----- Original Message -----
From: "David A. Case" <case.scripps.edu>
To: <amber.scripps.edu>
Sent: Thursday, June 10, 2004 7:51 AM
Subject: Re: AMBER: xleap solvatebox problem
> On Wed, Jun 09, 2004, Shan, Jufang wrote:
> >
> > I had the same problem as the one raised by Tom before.
> > http://amber.ch.ic.ac.uk/archive/200405/0357.html
> >
> > 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:
>
> What "C" compiler are you using? LEaP is entirely in C, and the fortran
> compiler you specified is not relevant here. If you are using gcc, please
> specify which version.
>
> We still have some RedHat 7.3 machines around, so maybe someone will be
> able to reproduce the problem, which is the first step to debugging it.
>
> >
> > I didn't experiece this problem using xleap from amber8 on SGI.
>
> Nor did I on various machines that I tried. At a minimum, use the SGI
vesion,
> at least when invoking the solvateBox command....
>
> ....regards...dac
>
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Received on Thu Jul 15 2004 - 16:53:00 PDT
