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
/
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 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..
Thank you
Asmi
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Received on Tue Jun 25 2013 - 00:30:02 PDT
