AMBER Archive (2004)

Subject: Re: AMBER: PMEMD Built ? Wont run..

From: Amber Administration (amber-admin_at_scripps.edu)
Date: Tue May 11 2004 - 16:15:14 CDT

Gary -
The one that jumps out at me is ntcm, which is no longer supported in sander
8 or pmemd 8. Everyone be on the lookout for this one, please. It is apt
to be in old mdin files (amber 7 and earlier). Sorry for the hassles on
this; we decided to do a bit of cleanup because the number of obsolete
control variables was getting out of hand, but I did sort of cringe over
just dropping them (kind of forces folks to peruse the amber 8 manual).
Regards - Bob Duke

PS - Amber guys - thanks for forwarding this stuff to the list; I am having
to use a dialin account because my broadband is hammered, and my mail seems
to be getting filtered.

----- Original Message -----
From: "Gary Waters" <gwaters_at_paracel.com>
To: <amber_at_scripps.edu>
Sent: Tuesday, May 11, 2004 1:36 PM
Subject: Re: AMBER: PMEMD Built ? Wont run..

> Hi Robert,
>
> Here is my input file; I did try changing the end to a / to no avail.
>
> Protein-Drug, complex: eq. ions+water w/200 ps MD, constant T,P.
> &cntrl
> imin = 0, ntx = 7, ntpr = 50, ntwx = 500,
> ntwe = 25, ntxo = 1,
> ntcm = 1, ndfmin = 6, nscm = 100,
> ntf = 2,
> ntb = 2, ntp = 1, pres0 = 1.0,
> ntc = 2, nsnb = 10,
> scee = 1.2, dielc = 1.0, scnb = 2.0,
> nstlim =100000,
> cut = 9.0,
> t =255.0, dt =.002,
> irest = 1,
> tempi = 300.0, temp0 =300., ntt = 1, dtemp = 0.0,
> tautp = 1.0, taup = 0.2, comp = 44.6,
> ig = 123442, pres0 = 1.0,
> nmropt = 0, ntr = 0,
> jfastw = 0
> &end
>
> Thanks,
> Gary Waters
>
> On Tue, 2004-05-11 at 10:25, Amber admin wrote:
> > From: "Robert Duke"
> > To: <amber_at_scripps.edu>
> > Subject: Re: AMBER: PMEMD Built ? Wont run..
> > Date: Tue, 11 May 2004 12:08:11 -0400
> >
> > Gary -
> > Looks like an invalid variable in the namelist. What are the contents
of
> > pmemd.in? Are all the variables things read by pmemd? Which version of
> > pmemd are you using? There can also be problems with the namelist
> > terminator on some systems, and variation in what f77 vs. f90 vs. f95
> > consider valid input. Thus some fortrans expect termination with &end,
> > others with /, and there can be different requirements for comments in
the
> > namelists (you have to read the compiler manual). Here though, I think
you
> > just have an invalid variable name.

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