Re: AMBER: solvatebox problem in the antechamber tutorial

From: David A. Case <>
Date: Wed, 9 Mar 2005 16:18:19 -0800

On Wed, Mar 09, 2005, Heiko Meyer wrote:

> I?m having a problem running the antechamber-tutorial:
> Everything works fine until generating the solvate box.
> 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.
> <>
> System:
> AMD Athlon XP
> Fedora Core 2

Which compiler are you using? If I understand correctly, this is a known
problem with the Portland Group C compiler. If you haven't already done so,
try using gcc to compile LEaP, and see if that helps.

(Other people on the list may have better/different suggestions here; this
is a really frustrating bug that has eluded solution for some time. It
happens only with some compiler/OS/machine combinations.

....good luck...dac

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Received on Thu Mar 10 2005 - 00:53:01 PST
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