[AMBER] [david.case.rutgers.edu: Re: Coordinate messed up after tleap set box]

From: David A Case <david.case.rutgers.edu>
Date: Tue, 4 Sep 2018 08:31:36 -0400

[Apologies if this appears twice: not sure what my email program was

On Mon, Sep 03, 2018, Simon Kit Sang Chu wrote:
> 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
> dimension
> saveamberparm cat $NAMEd.prmtop $NAMEd.inpcrd
> quit
> measure box dimension in vmd:
> measure minmax [atomselect all water]
> {-0.5879660844802856 -0.4595597982406616 -0.7424685955047607}
> {44.864402770996094 47.18324279785156 40.74130630493164}

I don't understand how this "measures box dimensions"? It looks like it
prints the largest and smallest of the water coordinates. What happens
if you just look at the final line of $NAMEd.inpcrd? That is where the
box dimensions are stored.

Note that "set <unit> box..." does not change any of the coordinates, nor
does it check if the box you are setting is appropriate. It simply adds
whatever box you ask for to the system. If you have a gap in the middle
of your system after a single step, I'm thinking that must have already
been there in the $NAMEc.pdb file: can you check that?


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Received on Tue Sep 04 2018 - 06:00:04 PDT
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