Hi,
Thanks for pointing that out. I changed the script to the following and it
now seems to work at the equilibration stage.
###############
source leaprc.gaff
source leaprc.ff99SBnmr
loadAmberParams frcmod.tip4pew
loadoff doc_final.lib
mol = loadpdb frame5_tryUS.pdb
charge mol
setBox vdw mol centers
savepdb mol frame5_complex_SOLVATED.pdb
saveamberparm mol frame5_complex.parm frame5_complex.crd
charge mol
quit
###############
The size of the box is inevitably different from the initial parent
trajectory. I take it that slightly different box sizes in the various
windows should not affect statistics calculated the umbrella sampling
calculation?
Also, as the system has already been equilibrated and minimised in the
parent trajectory, is it necessary to rerun a long minimisation and
equilibration in the different umbrella sampling windows?
Many thanks again.
On Thu, Aug 21, 2014 at 9:08 PM, David A Case <case.biomaps.rutgers.edu>
wrote:
> On Thu, Aug 21, 2014, George Green wrote:
>
> > setBox vdw {79.406 69.278 64.074}
>
> This is the wrong syntax. Type "help setBox" inside tleap to see the
> required
> arguments.
>
> You might want the "set <unit> box .... " command. See Section 12.5.38 of
> the Amber Reference manual for the syntax. (Unfortunately, the "help set"
> command in tleap is incomplete here; this should get fixed.)
>
> ....dac
>
>
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Received on Fri Aug 22 2014 - 10:30:03 PDT
