Hi,
Please send me the necessary files to reproduce the issue.
thanks,
scott
>
> On Thu, Mar 22, 2018 at 09:54:18AM +0900, Ikuo KURISAKI wrote:
> > Dear Dr. Mashaly, Prof. Case,
> >
> > I'd appreciate your kind replies.
> > Using octahedral box sounds one good option,
> > Although I still need to add > 100k water.
> > Then I will try AddToBox.
> > http://ambermd.org/tutorials/advanced/tutorial13/Solvation.html
> >
> > -----Original Message-----
> > From: Ahmed Mashaly [mailto:mashaly_1988.yahoo.com]
> > Sent: Wednesday, March 21, 2018 11:07 PM
> > To: AMBER Mailing List <amber.ambermd.org>
> > Subject: Re: [AMBER] upper limit of water with solvateBox
> >
> > Dear KURISAKI,
> > I have had a similar problem, this error was not reproducible with Dan.http://archive.ambermd.org/201802/0114.html
> >
> >
> > And yes I noticed that it happened with water +100 K molecule.Finally, we decided to go for an octahedral box with less amount of water, hope you can find another answer.
> > Kind Regards,Ahmed
> >
> >
> >
> > From: Ikuo KURISAKI <kurisaki.ncube.human.nagoya-u.ac.jp>
> > To: 'AMBER Mailing List' <amber.ambermd.org>
> > Sent: Wednesday, March 21, 2018 2:06 PM
> > Subject: [AMBER] upper limit of water with solvateBox
> >
> > Dear Ambers,
> >
> >
> >
> > Thank you for usual support.
> >
> > I have a question for upper limit of solvent number
> >
> > when we use solvatebox command of tLEaP.
> >
> >
> >
> > I tried to add > 100000 molecules to protein system, which give ca 300000 atoms
> >
> > By executing "solvateBox UNIT TIP3P 54".
> >
> > However, water molecules were not properly arranged in solvation box,
> >
> > Where the 'box' is not rectangular, rather have convex portion on the rectangular.
> >
> >
> >
> > This problem does not appear for smaller number of water molecules, i.e.
> > 90,000,
> >
> > In my case.
> >
> > Amber14 and 16 were employed, but both of them show the same results.
> >
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Received on Fri Mar 23 2018 - 10:00:02 PDT
