> Moreover, tleap tells me that it must apply some old-prep improper
> torsions, while sleap does not.
I doubt this is the case - it is probably comparing old-style to the
current ones. The old-style are read in prep files, but not used.
Bill
"Lachele Foley (Lists)" <lf.list.gmail.com> wrote:
> The old style impropers should be fine. I don't see obvious problems
> with the structure either.
>
> I'm running your simulation now in an attempt to reproduce the
> situation. Will get back to you.
>
> On Mon, Feb 20, 2012 at 9:54 AM, <tommaso.casalini.mail.polimi.it> wrote:
> > Hi all,
> > I tried both with tleap and sleap (AmberTools 1.4) and nothing changes.
> > I performed a quick simulation in implicit solvent and the hydrogen
> > issues still remain.
> > I observed the structure that leap gives to me, but I was not able to
> > find the incorrectly placed hydrogens.
> > Moreover, tleap tells me that it must apply some old-prep improper
> > torsions, while sleap does not.
> > Thank you for your help.
> >
> > Tommaso Casalini, Ph.D fellow
> > CFA lab, Politecnico di Milano
> >
> > Def. Quota David A Case <case.biomaps.rutgers.edu>:
> >
> >> On Sat, Feb 18, 2012, Karl N. Kirschner wrote:
> >>>
> >>> I have encountered a similar problem recently, I don't think it
> >>> involves the glycam06g force field directly, but something with how
> >>> xleap (didn't try tleap) interprets the force field when sourcing the
> >>> protein/dna force field. If you look at the output structure of leap,
> >>> I think you will see that a few of the hydrogen atoms are incorrectly
> >>> placed. I corrected this by only loading glycam06 parameters and
> >>> suppressing the the protein force field loading (i.e. xleap -s -f
> >>> leap.in). This then gave me the correct spatial structure of the
> >>> carbohydrate.
> >>
> >> Hi Karl:
> >>
> >> Thanks for the info. Can you post a specific example? We need to track this
> >> down. If LEaP is actually adding hydrogens in incorrect ways, it should be
> >> fixed. (I doubt that there is any difference between tleap and xleap, since
> >> most of their code is shared.)
> >>
> >> Are there other codes that are more reliable in adding hydrogens to
> >> carbohydrates? "Reduce" does a good job for proteins, but I
> >> doubt(?) that any
> >> third-party program would know about all the atom and residue names used by
> >> GLYCAM. Either you or someone else might check sleap, since it would be
> >> helpful to know if the latter worked better than tleap/xleap.
> >>
> >> ...thanks!...dave
> >>
> >> (cc-ing to amber-developers as well)
> >>
> >> _______________________________________________
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> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
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>
>
> --
> :-) Lachele
> Lachele Foley
> CCRC/UGA
> Athens, GA USA
>
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Received on Tue Feb 21 2012 - 09:30:02 PST
