On Thu, Jun 27, 2002, FyD wrote:
>
> I used "xleap" to generate "prmtop" and "prmcrd" files of an unusual
> unit. I checked the generated improper FF parameters with "rdparm". It
> looks like that an improper center has been selected for a CT atom type
> by xleap.
> See the output of rdparm just below:
> ....
> B 33: 1.000 3.14 2.0 :1_at_H1 :1_at_N1 :1_at_C6 :1_at_C2
> (2,1,11,3)
> ....
> Moreover, this oop is totally wrong topologically even if CT would be a
> C atom type. Indeed atom numbers 2, 1, 11 and 3 cannot make an improper
> dihedral....
I can't comment on this, since I don't know the topology of the molecule.
>
> I set up the CT atom type for C6 in the OFF library. See below:
> ....
> !entry.MOL.unit.atoms table str name str type int typex int resx
> int flags int seq int elmnt dbl chg
> ...
> "C6" "CT" 0 1 131073 11 6 0.020900
> ...
>
> After reading http://amber.ch.ic.ac.uk/Questions/improp.html,
> each sp2 atom should be an improper center; not a CT/sp3 atom type....
>
LEaP will consider putting a dihedral in for every atom with three neighbors;
it will actually do this only if there is an approriate entry in the parm.dat
file. Is it possible that your C6 atom has three bonded neighbors?
For sp2 atoms, it will print a warning (but still go on) if there appears
to be a "missing" improper torsion parameter in parm.dat; this is on the
assumption (not always valid) that sp2 atoms "should" have impropers.
..hope this helps.....dac
--
==================================================================
David A. Case | e-mail: case_at_scripps.edu
Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
The Scripps Research Institute | phone: +1-858-784-9768
10550 N. Torrey Pines Rd. | home page:
La Jolla CA 92037 USA | http://www.scripps.edu/case
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Received on Thu Jun 27 2002 - 08:33:16 PDT
