Hi Everyone,
I tried using the ParmEd and the '-xpsf' option in chamber to generate my
psf files.
ParmEd: chamber -top top_all36_prot-mod.rtf -param par_all36_prot-mod.prm
-psf step2_solvator.psf -crd step2_solvator.crd -nocmap -box
103.,103.,103.
Chamber: /usr/local/bin/chamber -top top_all36_prot-mod.rtf -param
par_all36_prot-mod.prm -xpsf step2_solvator.psf -crd step2_solvator.crd
-nocmap -vmd -box 103. 103. 103.
Then I perform a minimization, but I have trouble with the equilibration
step. I get the following error messages:
vlimit exceeded for step 0; vmax = 1208.7464
vlimit exceeded for step 0; vmax = 1208.7080
vlimit exceeded for step 0; vmax = 1208.8334
vlimit exceeded for step 0; vmax = 1208.9473
vlimit exceeded for step 0; vmax = 1208.8851
=====================================================================================
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= EXIT CODE: 11
= CLEANING UP REMAINING PROCESSES
= YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
=====================================================================================
APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal 11)
I don't have this problem when I generate the psf file using the '-psf'
option.
Chamber: /usr/local/bin/chamber -top top_all36_prot-mod.rtf -param
par_all36_prot-mod.prm -psf step2_solvator.psf -crd step2_solvator.crd
-nocmap -vmd -box 103. 103. 103.
Can someone explain what these error messages mean? Does it have to do
with the way I create the psf file?
Caitlin
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Received on Mon Oct 27 2014 - 06:30:02 PDT
