On Mon, Jun 21, 2004, Ting Wang wrote:
>
> I was trying to solvate my protein in xleap: solvateOct mol TIP3PBOX
> 12.0, I got more than 10K water molecules, the density > 3 g/cc, and the
> protein is not fully covered by water. But when I used amber7:
> solvateOct mol WATBOX216 12.0, I got 4391 wat and a density of 0.870
> g/cc and the protein is fully covered by wat.
>
> The machine/OS details :
>
> compilation: intel compilers on Intel(R) Xeon(TM) CPU 2.40GHz,Linux
> version 2.4.24 (gcc version 2.95.4 20011002 (Debian prerelease))
>
> Running: 1. the same machine as compilation.
> 2. AMD Athlon(tm) Processor 1.4GHz.Linux version 2.4.20 (gcc
> version 2.95.4 20011002 (Debian prerelease))
>
There have been several reports of this sort of behavior, but as far as I
know, no one who was willing to debug it has ever been able to reproduce it.
(I could not get anything like this to happen on my machines.)
It would be good to have the exact commands and protein structure you used,
since no one has ever posted a complete test case. But it may be that someone
will also have to dig up a machine with gcc 2.95.4 installed to see if this is
compiler-specific. Of course, if you have access to a machine with some
version of gcc 3, that would be the easiest course to check out such an idea.
....regards...dac
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Received on Mon Jun 21 2004 - 16:53:00 PDT
