Hi David,
I just check the pdb (attached) and there was no gap.
The pdb was actually converted from an inpcrd and prmtop because tleap only
accepts feeding in pdb. The AMBER format coordinate and topology files are
too big to send through the mailing list. If you don't mind, I can send it
to your email address directly. The box dimension is stored in
present.prmtop.
Regards,
Simon
David A Case <david.case.rutgers.edu> 於 2018年9月4日週二 上午5:29寫道：
> 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?
>
> ....dac
>
>
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Received on Tue Sep 04 2018 - 10:00:01 PDT
