Dear Amber
I am trying to run the NAMD with the amber force field
I have generated the prmtop and the inpcrd with xleap and solvated the
system with
solvatebox TIP3P 12 A
when i tried NAMD my protein comes out of the box and the water box got
splited
I fell the problem is owing to the cell basis vector 1 , 2 and 3 and the
cellorigin could be wrong
is the cell basis vector should be given as the last line of the inpcrd
file as vector 1, 2 and 3
what about the cell origin , how one can find it in amber generated files
can anyone give me some useful links or give me some suggestions since i am
trying it for the first time
thank you
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Received on Wed May 28 2014 - 08:30:02 PDT
