RE: [AMBER] Problem with solvationbox command

From: Ross Walker <>
Date: Tue, 23 Mar 2010 15:22:46 -0700

Hi Eric,

This is a known problem with earlier versions of AMBER and specific
compilers. E.g.

I suspect you are hitting the same compiler bug. The quickest solution would
probably be to download the latest copy of AMBERTools from the AMBER Website
and compile xleap in there using gnu or Intel compilers. The problem will
then likely go away.

Alternatively I would try recompiling AMBER 8 with a different set of

All the best

> -----Original Message-----
> From: [] On
> Behalf Of pellegrini
> Sent: Tuesday, March 23, 2010 6:11 AM
> To:
> Subject: [AMBER] Problem with solvationbox command
> Hello evrybody,
> I justed posted a few hours ago about a problem encountered when
> solvating a protein with a
> sugar-ligand. Sorry, but in my previous post, I was perhaps too fuzzy.
> Using the following commands on the first attached PDB file (ADA.pdb):
> source leaprc.ff99
> source leaprc.Glycam_06
> x = loadPDB ADA.pdb
> solvateBox x TIP3PBOX 10.0
> addions x Na+ 0
> saveAmberParm x ADA_Solvated.crd
> savePDB x ADA_Solvated.pdb
> creates a weird solvation box that does not surround the solute at all
> as you can see when looking at the second attached file
> (ADA_Solvated.pdb). Would you have any clue of what is (or I did) wrong
> with my setup ?
> thank you very much
> Eric

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Received on Tue Mar 23 2010 - 15:30:03 PDT
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