Dear all,
I am trying to minimize a protein which has aspartate, po4, glycerol , Nadp and
water in pdb file. I have generated prepin and frcmod file for all of the above
from antechamber as per tutorial and loaded them in tleap and saved the prmtop
and inpcrd file, but on miminizing the protein for 500 steps the minimization
stops at 230 step and gives the following error :
NSTEP ENERGY RMS GMAX NAME NUMBER
230 -2.2468E+04 1.2248E+04 9.9638E+05 O3P 5114
BOND = 358.4270 ANGLE = 826.4138 DIHED = 3289.6600
VDWAALS = -2513.4377 EEL = -25000.7354 HBOND = 0.0000
1-4 VDW = 1148.6144 1-4 EEL = -577.0991 RESTRAINT = 0.0000
Frac coord min, max: -0.338855902014186 1.12539885977885
Frac coord min, max: -0.338855902014186 1.12539885977885
The system has extended beyond
the extent of the virtual box.
Restarting sander will recalculate
a new virtual box with 30 Angstroms
extra on each side, if there is a
restart file for this configuration.
SANDER BOMB in subroutine Routine: map_coords (ew_force.f)
Atom out of bounds. If a restart has been written,
restarting should resolve the error
the input file used is :
Minimisation run
&cntrl
imin=1,
igb=0,
maxcyc=500,
ncyc=200,
ntmin=1,
ntpr=1,
ntb=0,
cut=10
/
I tried run a similar minimization with maxcyc=230 and the .out and .restrt file
were generated. Then i generated pdb (new7_mtb3_min12_pdb.pdb) for this restrt
file and visualized it in pdb. The O3P and H22 atom appeared to be overlapped.
However, they were not overlapped in the pdb generated from inpcrd file (
new7_mtb3_tleap.pdb) . The O3P and H22 are atoms of Nadp. Is there some problem
with the prepin file of nadp? I request you to kindly help me as where im going
wrong. Im attaching the two pdb file for ready reference.
Thanking you,
With regards,
Nicee.
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Received on Mon May 24 2010 - 03:00:10 PDT
