I just want to follow this up with what happened... for some reason when I combined the TIP3 MD trajectories into one for imin=5 processing, ptraj decided to screw with only 4 frames in the -middle- of one of the trajectories. Ptraj did not report any error when processing and the original trajectories are fine. So, point in hand, if for some reason anyone gets that error message... be sure to check the frame coordinates it failed on.
Trevor
________________________________________
From: Trevor Gokey [tgokey.mail.sfsu.edu]
Sent: Monday, September 27, 2010 2:25 PM
To: amber.ambermd.org
Subject: [AMBER] sander gb post-processing fail
Hello,
I got this line at the bottom (not sure if it's even an error) in my mdout file while using sander.MPI (Amber11) to post process and trajectory.
NSTEP ENERGY RMS GMAX NAME NUMBER
1 1.7936E+02 1.7701E+02 5.7539E+03 SG 2696
BOND = 693.8115 ANGLE = 1705.4697 DIHED = 2288.0264
VDWAALS = 2873.7781 EEL = -15679.1151 EGB = -2811.2453
1-4 VDW = 738.9313 1-4 EEL = 10289.4658 RESTRAINT = 0.0000
ESURF = 80.2363
minimization completed, ENE= 0.17935881E+03 RMS= 0.177014E+03
minimizing coord set # 56129
iatenvcnt .gt. iemax in icosasurf
and it just quit with no other warning as far as I can tell. I've ran a previous trajectory successfully with the same input, which I extracted from mmpbsa.py (except the ioutfm=1 part):
1ANE 115 ns
&cntrl
ntb=0, idecomp=0, cut=999.0, nsnb=99999,
imin=5, maxcyc=0, ncyc=0, igb=5,
saltcon=0, intdiel=1, extdiel=78.3,
gbsa=2, surften=0.0072,ioutfm=1
&end
What should I do seeing an error like that? The only thing I can extrapolate from the error message is that the (i)nternal(e)nergymax in icosasurf(surften issue) has something wrong. Am I far off?
Thanks,
Trevor Gokey
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Received on Fri Oct 01 2010 - 12:30:03 PDT
