AMBER Archive (2009)

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

From: mousumi (mousumi_at_mmb.pcb.ub.es)
Date: Thu Oct 22 2009 - 00:20:48 CDT

Thanks a lot to all of you !!

On Wed, 21 Oct 2009 08:28:58 -0400, Brent Krueger <kruegerb_at_hope.edu>
wrote:
> 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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>>
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