Hi, sorry if I answer only now!
I have run the mmpbsa.in script (show below) using this command: $
MMPBSA.py -O -i mmpbsa.in -o result.dat -cp bestW.tpp -y md3.coord >
progress.log
mmpbsa.in
--------------------------------------------------------------------
&general
endframe=2, keep_files=2,
/
&nmode
nmstartframe=1, nmendframe=2,
nminterval=1, nmode_igb=0, nmode_istrng=0.1,
/
---------------------------------------------------------------------
It works and produces some temporary files (such as
_MMPBSA_complex.mdcrd.0, _MMPBSA_dummycomplex.inpcrd ......), but after it
crashes and in terminal the following message returns:
FATAL: allocation failure in ivector()
CalcError: /usr/local/amber12/bin/mmpbsa_py_nabnmode failed with prmtop
bestW.tpp!
Exiting. All files have been retained.
Here I report the progress.log:
Loading and checking parameter files for compatibility...
Preparing trajectories for simulation...
2 frames were processed by cpptraj for use in calculation.
2 frames were processed by cpptraj for nmode calculations.
Running calculations on normal system...
Beginning nmode calculations with /usr/local/amber12/bin/mmpbsa_py_nabnmode
calculating complex contribution...
cpptraj found! Using /usr/local/amber12/bin/cpptraj
mmpbsa_py_nabnmode found! Using /usr/local/amber12/bin/mmpbsa_py_nabnmode
Can you help me to understand where I make a mistake?
Thank you
2016-11-17 15:54 GMT+01:00 Nhai <nhai.qn.gmail.com>:
>
>
> Please be much more specific. E.g: what "doesn't work" mean here? What is
> exactly you did?
>
> Hai
>
> > On Nov 17, 2016, at 8:47 AM, Imma Speciale <i.spec88.gmail.com> wrote:
> >
> > ---------- Forwarded message ----------
> > From: Imma Speciale <i.spec88.gmail.com>
> > Date: 2016-11-17 14:36 GMT+01:00
> > Subject: Normal Mode Analysis
> > To: amber-bounces.ambermd.org
> >
> >
> > Hi,
> > I want to calculate the normal mode of my protein, using amber12.
> > I have tried with mmpbsa, but it doesn't work, maybe why it plans the
> > usage
> > of complex and ligand, and I have only one protein. I have also tried
> to
> > construct the covariance matrix, but without results.
> > Someone can help me suggesting a method to calculate these modes??
> > Thanks
> > Imma
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
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Received on Tue Nov 22 2016 - 03:00:04 PST
