AMBER Archive (2009)

Subject: Re: [AMBER] "extra points" incompatibility with pmemd

From: Brent Krueger (kruegerb_at_hope.edu)
Date: Wed Oct 21 2009 - 07:28:58 CDT

Or maybe you don't want extra points at all? Do you know what they are for
and why you might want them?

If so, then upgrade as Bob has suggested. If not, then you should go back
and solvate your system with something that does not include extra points
like TIP3P water.

Brent

On Wed, Oct 21, 2009 at 8:02 AM, Robert Duke <rduke_at_email.unc.edu> wrote:

> Extra points are available in pmemd in amber 10. The implementation is
> significantly faster than what is available in sander 9; if you are going to
> use extra points much at all, it is probably worth upgrading to amber 10 so
> you get extra points support in pmemd.
> Regards - Bob Duke (the guy who did it)
> ----- Original Message ----- From: "mousumi" <mousumi_at_mmb.pcb.ub.es>
> To: <amber_at_ambermd.org>
> Sent: Wednesday, October 21, 2009 3:57 AM
> Subject: [AMBER] "extra points" incompatibility with pmemd
>
>
>
> Dear all,
>
> I am trying to simulate a system containing DNA and ions using PMEMD. The
> system has been solvated using the frcmod.tip4pew forcefield and TIP4PEWBOX
> water box. After the normal minimization and equlibration with "sander"
> when I am going for the MD production run, its giving me the error "PMEMD
> cannot process prmtop files with extra points data! Please use sander 9.0
> instead" and then stopped running. Please let me know what I should do to
> avoid the error.
>
> Thanks in advance,
> Mousumi
>
>
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-- 
_______________________________________________
Brent P. Krueger.....................phone:   616 395 7629
Associate Professor................fax:       616 395 7118
Hope College..........................Schaap Hall 2120
Department of Chemistry
Holland, MI     49423
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