On Tue, Jun 25, 2013 at 3:07 AM, Asmita Gupta <asmita4des.gmail.com> wrote:
> Dear users,
>
>
> I want to do some stability calculations on an RNA aptamer structure using
> MMPB(GB)/SA calculations. there are no ligands,so it's just a single
> species in the system.
>
> I submiited the following script for free energy and nmode analysis:
>
> Input file for running GB/nmode
> &general
> debug_printlevel=3,interval=10,netcdf=1
> # entropy=1,
> /
> &gb
> igb=5, saltcon=0.100
> /
> &decomp
> idecomp=1
> /
> &nmode
> maxcyc=1000,nminterval=10,nmode_igb=1,nmode_istrng=0.1
> /
>
Just an opinion, FWIW -- I am skeptical of GB's treatment of RNA
(especially igb=2, 5, and 7 where no effort was made to tune it to nucleic
acids). With igb=2 I don't know that I'd even trust the qualitative results
of RNA stability with two different conformations. The problem is that the
solvation free energy for such highly-charged systems is incredibly large,
so you're looking for a small difference by subtracting very large
numbers...
> and subsequently,
>
> MMPBSA.py -O -i mmpbsa.in -o results_gb_decomp_nmode.dat -sp pc.prmtop -cp
> pc_stripped.prmtop -y ../../production/run_10.crd -do decomp.out -eo
> energy.out -deo decomp_energy.out
>
> so i have basically given solvated topologies and because it's a single
> molecule, a dry topology file for -cp option....is this method run
> correct??
>
A couple comments here. Depending on how large your system is, 100 frames
of nmode calculations could take weeks to finish. Also, setting maxcyc to
1000 is probably not good enough to ensure proper convergence to a local
minimum. The default is 10000, which may still be too small -- you should
test on one or two frames to be sure.
>
> a total of 1000 frames will be analyzed in this process...
>
> my problem is after submitting it, the process just keeps on going, and now
> i am getting this message:
>
> Line minimizer aborted: step at upper bound 0.06053411
> Line minimizer aborted: step at upper bound 0.10156325
> Line minimizer aborted: step at upper bound 0.080443891
> Line minimizer aborted: step at upper bound 0.069342559
> Line minimizer aborted: step at upper bound 0.083281256
> ...
> ..
>
> .....is it a normal behaviour?? To me it seems that the minimization
> process in nmode is going wrong somewhere...Pl suggest..
>
The minimization is getting stuck. The system may be complex, and while it
knows that there is a move that will take it to a lower energy, it can't
seem to find it. If the defaults cannot minimize your structure, you may
need to modify mmpbsa_energy.nab (in $AMBERHOME/AmberTools/src/mmpbsa_py/)
and reduce the size of the coordinate move (xo.ls_maxatmov -- it is
described on page 515 of the AmberTools 13 manual).
This is just an idea, I've never actually had this problem before. Note if
you reduce the step size, however, it will take far more minimization steps
(and many more cycles) to minimize your system. I would also evaluate
whether or not a normal mode calculation is really necessary here, and why
you are running it. It may not be important for what you're trying to
learn...
Good luck,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Jun 25 2013 - 05:00:04 PDT
