Hello,
I am trying to set up an umbrella sampling analysis of a drug entering a
protein. I already have an imaged and rms fitted trajectory file that shows
the binding process and intend to strip suitable frames ~0.4 angstroms
apart.
As the desolvation process during the binding event is important, I would
prefer to use all the waters from the initial file.
So to setup the simulations in every umbrella sampling window, I stripped
out the pdb waters and ran the following tleap script:
#############
source leaprc.gaff
source leaprc.ff99SBnmr
loadAmberParams frcmod.tip4pew
loadoff doc_final.lib
mol = loadpdb frame5_tryUS.pdb
charge mol
setBox vdw {79.406 69.278 64.074}
savepdb mol frame5_complex_SOLVATED.pdb
saveamberparm mol frame5_complex.parm frame5_complex.crd
charge mol
quit
###############
The questions I had were:
1) If i use setbox vdw to recreate the box around all the solvent atoms, do
I use "Total vdw box size:" as input to recreate the original values?
2) The setbox command I have above do not seem to add the box simensions
at the end of the inpcrd file and i have to add these manually. This works
fine for minimisation, but fails during equilibration as ifbox=0. I guess
this is a setting in the parm file? Could anyone help me with the correct
command to this?
Many thanks
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Received on Thu Aug 21 2014 - 12:30:02 PDT
