Hi,
On Wednesday, July 3, 2013, Jason Swails wrote:
>
> Have you compared the python mask selection and the one from cpptraj and
> ambmask, too?
Just to follow up on what Jason said, you can do a quick test mask with the
'select' command in cpptraj:
select <mask>
This will print the atom #s corresponding to the atom mask.
-Dan
>
>
> >
> > I guess I can just do this by hand in tleap.
> >
> > Brian
> >
> >
> > On Tue, Jul 2, 2013 at 3:45 AM, FyD <fyd.q4md-forcefieldtools.org<javascript:;>>
> wrote:
> >
> >> Dear Brian,
> >>
> >> There is no difficulty for differentiating the 'HC' atom type vs the
> >> 'H1', 'H2' or 'H3' ones; i.e. is a given hydrogen atom, which is
> >> connected to a carbon atom connected to one, two or three heteroatoms.
> >> The same rule applies for the aromatic hydrogens 'HA', vs 'H4' and
> >> 'H5'... These 'HC' vs 'H1'/'H2'/'H3' and 'HA' vs 'H4'/'H5' definitions
> >> are at the basis of the Cornell et al. force field; and there is no
> >> difficulty for coding that...
> >>
> >> R.E.D. Python fully handles this quite basic problem (differentiating
> >> the different double bonds is far more complex for instance); I invite
> >> you to use R.E.D. Python when available i.e. sometimes next
> >> September/October 2013.
> >> You can also use R.E.D. Server and request a private assistance to
> >> post-process your data with R.E.D. Python.
> >>
> >> regards, Francois
> >>
> >>
> >>> I'm running calculations on a bunch of nucleic acids and analogues.
> Since
> >>> these are non-standard non-nucleobase compounds I used antechamber to
> >>> assign atom types. However, it would appear that the hydrogen
> >> Lennard-Jones
> >>> parameters for atoms of the same type do not match in prmtops generated
> >>> from antechamber files and those from leaprc.ff10
> >>>
> >>> (using parmed.py printDetails)
> >>> Rmin/2 epsilon
> >>> type AC FF10 AC FF10
> >>> H4 1.4870 1.4090 0.0157 0.0150
> >>> HA 1.4870 1.4590 0.0157 0.0150
> >>>
> >>> I'm guessing I messed something up here by reloading parameters.
> Should I
> >>> not be creating a new frcmod? Still, I find it weird that two atoms
> would
> >>> have the same type but different parameters. Where does the flag "-at
> >>> amber" get parameters from? I assumed these would be the same LJ types
> >> that
> >>> have been around since FF94.
> >>
> >>
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org <javascript:;>
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> >
> > --
> > ================================ Current Address =======================
> > Brian Radak : BioMaPS
> > Institute for Quantitative Biology
> > PhD candidate - York Research Group : Rutgers, The State
> > University of New Jersey
> > University of Minnesota - Twin Cities : Center for
> Integrative
> > Proteomics Room 308
> > Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
> > Department of Chemistry : Piscataway, NJ
> > 08854-8066
> > radak004.umn.edu <javascript:;> :
> > radakb.biomaps.rutgers.edu <javascript:;>
> > ====================================================================
> > Sorry for the multiple e-mail addresses, just use the institute
> appropriate
> > address.
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org <javascript:;>
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> --
> Jason M. Swails
> Quantum Theory Project
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org <javascript:;>
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Wed Jul 03 2013 - 06:00:04 PDT
