[AMBER] Coordinate messed up after tleap set box

From: Simon Kit Sang Chu <simoncks1994.gmail.com>
Date: Mon, 3 Sep 2018 12:31:32 -0700

Hi everyone,

I want to do a TI calculation while setting the box dimension. I did it in
tleap but the coordinates are messed up after 1 step simulation.

tleap input:

source leaprc.protein.ff14SB
source leaprc.water.tip3p
cat = loadpdb $NAMEc.pdb (already solvated and I must do it this way)
set cat box {4.41467930E+01 4.67352440E+01 4.01360530E+01} # add box
saveamberparm cat $NAMEd.prmtop $NAMEd.inpcrd

measure box dimension in vmd:

measure minmax [atomselect all water]
{-0.5879660844802856 -0.4595597982406616 -0.7424685955047607}
{44.864402770996094 47.18324279785156 40.74130630493164}

Slightly different from the set box information I fed.

I also notice a gap in the middle of the box after simulation. Is it a bug
in set box in tleap? Feel free to ask me for the topology and coordinate

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Received on Mon Sep 03 2018 - 13:00:02 PDT
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