Like Jason said, I also don't recommend people to use igb=1,2,5,7 or even 8
in Amber to perform MM-GBSA analysis for nucleic acid system since they
were not tuned in for such a kind of system. We have done many PB
calculations (using Delphi) for various DNA, RNA structures and found
significant difference between those GB models and PB (even few hundred
kcal/mol difference).
Our lab have been working on fitting parameters for nucleic acid and got
some promising results. Hopefully we can finalize our optimization and
introduce the set to next Amber release.
Hai Nguyen
On Tue, Jun 25, 2013 at 7:48 AM, Jason Swails <jason.swails.gmail.com>wrote:
> 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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>
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Received on Tue Jun 25 2013 - 13:30:02 PDT
