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.
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Received on Tue Jul 02 2013 - 01:00:02 PDT
