I have encountered the following error (the last few lines of the output
file have been included below) when running minimization using pmemd.MPI on
an 8-processor node.
======= output file contains ===============
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
default_name
General flags:
imin = 1, nmropt = 0
Nature and format of input:
ntx = 1, irest = 0, ntrx = 1
Nature and format of output:
ntxo = 1, ntpr = 50, ntrx = 1, ntwr =
500
iwrap = 0, ntwx = 0, ntwv = 0, ntwe =
0
ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat=
0
Potential function:
ntf = 1, ntb = 0, igb = 1, nsnb =
25
ipol = 0, gbsa = 0, iesp = 0
dielc = 1.00000, cut = 16.00000, intdiel = 1.00000
saltcon = 0.00000, offset = 0.09000, gbalpha= 1.00000
gbbeta = 0.00000, gbgamma = 0.00000, surften = 0.00500
rdt = 0.00000, rgbmax = 25.00000 extdiel = 78.50000
alpb = 0
Frozen or restrained atoms:
ibelly = 0, ntr = 0
Energy minimization:
maxcyc = 2400, ncyc = 50, ntmin = 1
dx0 = 0.01000, drms = 0.00010
| Intermolecular bonds treatment:
| no_intermolecular_bonds = 1
| Energy averages sample interval:
| ene_avg_sampling = 1
Error: ifbox=2 in prmtop but angles are not correct
Input errors occurred. Terminating execution.
==============================================
the corresponding input file used looks like this:
Initial minimization of the pdb complex in 1WBS
&cntrl
imin=1, maxcyc=2400, ncyc=50,
cut=16, ntb=0, igb=1,
&end
====================
I was successful in executing the minimization of the same system on a
single processor machine without the above error.
I would like to know about any suggestions about what could be going wrong
with this submission.
thanks very much,
Shashi Rao
--
Shashidhar N. Rao
3 SERINA DRIVE
PLAINSBORO
NEW JERSEY 08536 USA
shashidharr.gmail.com
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Received on Wed Jan 23 2013 - 12:30:03 PST
