On Mon, Jan 13, 2003, Layi Adekoya wrote:
> I had first ran antechamber to generate the charges
> for the ligand. I soured leaprc.gaff.
> I loaded the prep input files and that
> of the parameters ( frcmod).
> sourced leaprcff.94 for the protein.
> make bond unit.1.* unit.2.* (to make the bond between ligand and protein)
> set unit.1.* type ~ (to change atom type after making bond)
> saveamberparm unit *.top *.crd
> then it crashes. it does write the *.top file but not the
> *.crd file.
> I checked all the bonds made and the types and all was rightly
> done.
> It was just at the last command that it crahsed.
>
I still think we need the *exact* commands you used; for example the above
summary does not indicate where the protein coordinates came from. Also,
with all of the "*" and "~" shorthand, you are really telling us more what
you *intended* to do, not what you really did.
If you are reluctant to send these, (or even not), try leaving out the
"make bond" command [whatever that really means--there is no "make" command
in LEaP], and the following "set" command, to see if that can help narrow
down the problem.
..good luck..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 Mon Jan 13 2003 - 09:08:15 PST
