I reinstalled AmberTools12 (what I should have done in first place). Both
xleap and tleap work just fine.
Sorry for the trouble.
2014-03-26 18:33 GMT+01:00 David A Case <case.biomaps.rutgers.edu>:
> On Wed, Mar 26, 2014, Ilias Patmanidis wrote:
> >
> > 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.
>
> I cannot reproduce the problem. With xleap, I get the box info at the end
> of
> the crd file. I really suspect operator error here: tleap and xleap share
> the
> same code, and it is very hard to see how xleap and tleap could be giving
> different answers. Also, if this simple workflow were failing, everyone on
> the Amber list would be posting problem reports. Can you double-check that
> you used exactly the same commands in xleap as in tleap?
>
> Is the *only* difference between xleap and tleap the box info? Are the
> prmtop
> files different at all?
>
> ...dac
>
>
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>
--
Ilias Patmanidis
MSc student in Bioinformatics and data analysis in biology,
University of Geneva, Switzerland
Tel(mob):
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Received on Thu Mar 27 2014 - 04:00:03 PDT
