Dear all,
I have a question regarding the setBox command used in preparing input
typologies for TI calculation in side-chain mini tutorial.
complex = combine {m1 m2 ligand w}
set default nocenter on
# create protein in solution
setBox protein vdw {32.71 31.46 43.84}
savepdb protein protein.pdb
I had been looking in the manual for setBox command, and it is not
clear if these values are the dimension of the box or center of the
box ? Looking at solvatebox, it looks like it is dimension of the box.
Anyways, I want to make sure that I not doing any mistake, so I
explain what I am doing. I used solvateBox to add water in the
wild-type protein and saved only water and ions in water_ions.pdb
file. Now, I use total vdw box size {59.898 76.664 63.740} value
when solvating system with water_ions.pdb.
> tleap-printed following upon solvateBox:
total atoms in file: 1847
Solute vdw bounding box: 34.561 51.395 38.994
Total bounding box for atom centers: 56.561 73.395 60.994
Solvent unit box: 18.774 18.774 18.774
Total vdw box size: 59.898 76.664 63.740 angstroms.
Is that okay ?
One more query related to TI support in pmemd (cuda) in Amber16.
There is no mentioning of it in the manual so I believe cuda version
still does not support TI ?
Thanks,
Mish
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Received on Wed Jun 08 2016 - 19:00:02 PDT
