AMBER Archive (2004)

Subject: Re: AMBER: solvate proteins in xleap/amber8

From: Tomas Kubar (tomas.kubar_at_uochb.cas.cz)
Date: Tue Jun 22 2004 - 02:44:54 CDT

David A. Case wrote:
> 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.
>
> There have been several reports of this sort of behavior

Yes. Recently, I encountered this problem as well. After having loaded a
parameter set explicitly (> source leaprc.ff94, os something like that),
everything went fine.

tomas
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