From: Simon Watson (simon.watson_at_ucl.ac.uk)
Date: Tue Jan 09 2007 - 12:06:53 CST
I have seen that several other people on this forum have been
affected by the same problem; I have followed all the threads, and
attempted all the suggestions but I am still suffering from the same
My system is composed of HIV protease, bound to saquinavir, in a
water box 81.93Å by 90.55Å by 81.80Å. The PME grid size was
originally 81 by 90 by 81 (x,y,z), and the protein and ligand are
restrained during the minimisation. When I tried minimising, I
attained the following output:
ERROR: Stray PME grid charges detected: 0 sending to 7 for planes 18 19
ERROR: Stray PME grid charges detected: 0 sending to 6 for planes 16 17
ERROR: Stray PME grid charges detected: 0 sending to 23 for planes 63
ERROR: Stray PME grid charges detected: 0 sending to 22 for planes 60
Warning: Bad global exclusion count, possible error!
Warning: Increasing cutoff during minimization may avoid this.
Warning: Bad global bond count!
Warning: Bad global angle count!
Warning: Bad global dihedral count!
Warning: Stray PME grid charges ignored!
PRESSURE: 122 -1.47246e+07 1.52151e+06 -1.38893e+06 1.5201e+06
-1.57702e+07 282057 -1.39157e+06 279814 -1.32042e+07
GPRESSURE: 122 -2.35315e+08 -1.20036e+07 1.84397e+07 -1.2128e+08
5.7502e+06 -6.52172e+07 -5.55886e+07 6.14859e+06 -3.7112e+07
ENERGY: 122 99999999.9999 256946.1353 8404.9533
0.0000 -1499602.7597 1171537.4338 492703.9185
0.0000 0.0000 99999999.9999 0.0000
99999999.9999 99999999.9999 0.0000 -14566345.2938
-88892404.2323 606823.5931 -14566345.2938 -88892404.2323
I have attached my minimisation configuration file. This is the
first time I have tried simulating with a ligand - all previous
simulations were apo-proteins. For this reason I have had to set up
the system in AMBER, though I am simulating with NAMD.
As suggested, I tried increasing the cutoff from 12 to 14, 16, 18,
but this didn't help. I also tried increasing the size of the PME
grid, ensuring it stayed a multiple of 2,3 and 5 in each direction,
but this also didn't help.
I found on the NAMDWiki Troubleshooting page that it could be because
of an atom (probably hydrogen) moving to the other side of the cell,
making a bond extend across the cell. I loaded up the .pdb and .crd
file in VMD and didn't see any very long bonds, except for 4 at the N-
terminal amino acid that extend out very far out of the box, but
these are present even in different simulations that run with no
problems. I also checked for uninitialised coordinates, but they all
I am not an experienced user of NAMD, and so was hoping that someone
could shed some light on any mistakes I have made or potential fixes
I have overlooked..
Thank you, in advance, for any help.
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