By the way, solvating before addions will give better packing.
Bill
Ilias Patmanidis <patmanidis.ilias.gmail.com> wrote:
> Dear AMBER users,
>
> I was using xleap to generate topology and coordinate files for a specific
> system
>
> >source leaprc.ff12SB
> >loadamberparams frcmod.ionsjc_tip3p
> >test = loadPDB test.pdb
> >addions test Na+ 2
> >solvatebox test TIP3PBOX 10
> >savePDB test test1.pdb
> >saveamberparm test test.prmtop test.crd
>
> Information about the vdw box size was missing from the end of the
> generated test.crd.
>
> This problem did not appear in tleap. The same commands gave a different
> output with the vdw box size included in the end of the file.
>
> Best regards,
> Ilias Patmanidis
>
> --
> Ilias Patmanidis
> University of Geneva, Switzerland
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Received on Tue Apr 01 2014 - 17:00:02 PDT
