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.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.
> Regards - Bob Duke
>
> ----- Original Message -----
> From: "Gary Waters" <gwaters.paracel.com>
> To: <amber.scripps.edu>
> Sent: Tuesday, May 11, 2004 12:00 PM
> Subject: AMBER: PMEMD Built ? Wont run..
>
>
> > Hi Everyone,
> >
> > I believe I built pmemd correctly with mpich.
> > On mpich I can do some of the example and test runs fine, with no
> > errors. Then I go over to pmemd and run my script, and get these
> > errors. I do not know what is going on, can someone shed some light on
> > my dilemma ?
> >
> > forrtl: severe (19): invalid reference to variable in NAMELIST input,
> > unit 5, file /export/bionumerik/pmemd.in
> > Image PC Routine Line Source
> > pmemd 0811333F Unknown Unknown Unknown
> > pmemd 080DF9AB Unknown Unknown Unknown
> >
> > Stack trace terminated abnormally.
> > p2_29314: p4_error: net_recv read: probable EOF on socket: 1
> > p10_11492: p4_error: net_recv read: probable EOF on socket: 1
> > bm_list_17110: (0.444700) wakeup_slave: unable to interrupt slave 0 pid
> > 17109
> > bm_list_17110: (0.444772) wakeup_slave: unable to interrupt slave 0 pid
> > 17109
> > p9_11334: p4_error: net_recv read: probable EOF on socket: 1
> > p15_9668: p4_error: net_recv read: probable EOF on socket: 1
> >
> > --
> > Thanks,
> > Gary Waters
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Received on Tue May 11 2004 - 18:53:00 PDT
