HD is something I created, and yes, it did not have element info. as 'H'
in the .prepi file. I just checked out the leaprc.ff99 file, and for
every H-type in the parm99.dat file, the element is defined as 'H',
except for HZ-type. Seeing that 'HZ' type is defined in the parm99.dat
file with hydrogen parameters, I assumed that HZ is another type for
hydrogen.
---------------- taken from parm99.dat --------------------------
HZ 1.008 0.161 H bond sp C (Howard et
al.JCC,16,243,1995)
-----------------------------------------------------------------
I do not know where 'HZ' is used, but if leaprc.ff99 is using the
parm99.dat parameters, 'HZ' should be CLEARLY specified, including the
element info.
On Sun, 19 Mar 2006, David A. Case wrote:
> On Sun, Mar 19, 2006, Ilyas Yildirim wrote:
>
> > I have changed the dummy atom type from DH to HA, H and HZ (also HD).
For
> > HA and H, both threads gave the same results. For HZ and HD, it gave
> > different results, and the system blows up at the end. I use the same
> > extra.frcmod file (except changing the atom type). Here is the .frcmod
> > file I am using (the first parts which has the bond info.s in it):
> > -----------------------------------------------------
> > MASS
> > HZ 1.008
> >
> > BOND
> > O -HZ 434.0 1.010 [N2-H]
> > CA-N* 424.0 1.383 [C-N*]
> > .
> > .
> > .
> > -----------------------------------------------------
> > Originally, it was
> >
> > O -DH 434.0 1.010 [N2-H]
> >
> > I have changed this atom type to H, HA, HZ, and HD.
> >
> > I think that SHAKE is turning on the SHAKE constraints of specific
> > hydrogen types, not all H-types. I would like to know if this is true.
>
> (a) Use the code, Luke! I'm serious: you need to gain confidence in
your
> *own* ability to answer questions like these by examining the code to
> understand how it works. Often, all you need is some extra print
statements
> to give more detailed information.
>
> (b) My guess: you don't mention anything about what "addAtomTypes"
commands
> you are giving to LEaP. The leaprc.ff99 file defines HA and H as
element "H",
> but says nothing about HZ and HD. So, if you used this leaprc, and
didn't do
> additional work, it probalby doesn't think HZ is hydrogen (what is HZ,
> anyway?) It's the element that is key, not the mass, or the name, or
anything
> else. You have to make sure that LEaP knows about the atom types you
are
> using, and associates them correctly with elements.
>
> ...dac
>
>
--
Ilyas Yildirim
---------------------------------------------------------------
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---------------------------------------------------------------
Received on Wed Apr 05 2006 - 23:49:36 PDT
