Thanks for the quick replies.
On closer inspection it would appear that all hydrogens are getting typed
correctly (*i.e.* the specific type is indicative of the connectivity), but
hydrogens bound to carbon all get the "HC"-type LJ parameters (hydrogens
bound to nitrogen are just fine). I don't have much interest in figuring
out what is going on in PARMCHK.DAT in order to fix this (does anybody know
what the tables in there mean?).
Fortunately parmed should let me just correct the LJ parameters based on a
type selection. Unfortunately, I'm not sure the ".%" ambmask syntax is
working properly in the Python implementation at the moment and Jason is
out of the office for the week.
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> 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
> 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 :
radakb.biomaps.rutgers.edu
====================================================================
Sorry for the multiple e-mail addresses, just use the institute appropriate
address.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jul 02 2013 - 07:00:02 PDT
