On Mon, Sep 14, 2015 at 8:50 AM, Damiano Spadoni <enxds6.nottingham.ac.uk>
wrote:
> Hi,
>
> as I'm having lot of fun with this my last simulation, I'll show you my
> results following your suggests (adding commas, taking out blank spaces and
> using group restraints too), but it's been for days now that I'm receiving
> the last error text (the best one in my opinion):
>
> nstlim = 500000, dt = 0.002,
> ioutfm=1, iwrap=1,
> ntpr=500, ntwx=500, ntwr=1000,
> restraintmask=':1639, 1642, 1645, 1648',
> restraint_wt=1.0
> vlimit=2.0, nmropt=1,
> /
> &wt type='END'
> /
> Hold Fe4S4
> 50.0
> RES 1639 1648
> END
> END
>
> Begin reading energy term weight changes/NMR restraints
> WEIGHT CHANGES:
> ** No weight changes given **
>
> RESTRAINTS:
> No valid redirection requests found
>
>
> ioutfm=1, iwrap=1,
> ntpr=500, ntwx=500, ntwr=1000,
> restraintmask=':1639, 1642, 1645, 1648',
> restraint_wt=1.0
> vlimit=2.0
> /
> &wt type='END'
> /
> Hold Fe4S4
> 50.0
> RES 1639 1648
> END
> END
>
> | ERROR: PMEMD does not support intermolecular PRFs!
>
>
>
> tempi=300.0, temp0=300.0,
> ntt=3, ig=-1, gamma_ln=1.0,
> nstlim = 500000, dt = 0.002,
> ioutfm=1, iwrap=1,
> ntpr=500, ntwx=500, ntwr=1000,
> /
> &wt type='END'
> /
> Hold Fe4S4
> 50.0
> RES 1639 1648
> END
> END
>
> ----- READING GROUP 1; TITLE:
> Hold Fe4S4
>
> GROUP 1 HAS HARMONIC CONSTRAINTS 50.00000
> GRP 1 RES 1639 TO 1648
> Number of atoms in this group = 182
> ----- READING GROUP 2; TITLE:
> END
>
> GROUP 2 HAS HARMONIC CONSTRAINTS 0.00000
>
> rfree: End of file on unit 5
>
>
>
> tempi=300.0, temp0=300.0,
> ntt=3, ig=-1, gamma_ln=1.0,
> nstlim = 500000, dt = 0.002,
> ioutfm=1, iwrap=1,
> ntpr=500, ntwx=500, ntwr=1000
> /
> Hold Fe4S4
> 50.0
> RES 1639 1648
> END
> END
>
> default_name
> ----- READING GROUP 1; TITLE:
> Hold Fe4S4
>
> GROUP 1 HAS HARMONIC CONSTRAINTS 50.00000
> GRP 1 RES 1639 TO 1648
> Number of atoms in this group = 182
> ----- READING GROUP 2; TITLE:
> END
>
> GROUP 2 HAS HARMONIC CONSTRAINTS 0.00000
>
> rfree: End of file on unit 5
>
I am really confused here. Where is all of this output coming from? Is
it all in the same file? It seems like the same section is printed several
times, but slightly differently -- it almost seems like you're trying to
run pmemd in parallel, but with pmemd instead of pmemd.MPI (but I don't
know, since I don't know what command you used to run the calculation).
The input file appears to be truncated, since it doesn't have a title line
or a &cntrl header to indicate the start of the &cntrl namelist. Also, the
output here suggests that rfree (which is the free-format input parser used
to parse the cards that follow the namelists) is expecting more input and
is failing when it hits the end of the input file, but I can't see anything
. The other error (about intermolecular PRFs) indicates a broken prmtop
file (use the checkValidity command in ParmEd to make sure your prmtop file
doesn't have problems).
To be honest I'm having a hard time understanding what you're showing
here. Just doing a partial dump of output without giving more complete
context makes it difficult to help.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Sep 14 2015 - 06:30:03 PDT
