AMBER Archive (2004)

Subject: Re: Re: AMBER: Does this warning matter? (about improper torsion parameters)

From: J. Zhang, Dr (
Date: Wed May 19 2004 - 20:57:35 CDT

Dear David A. Case,

        Thank you very much!!!

Best Regards,

J. Zhang, Dr
Institute of Biophysics
Nanjing University

>On Wed, May 19, 2004, J. Zhang, Dr wrote: >> >> When I tried to create topology file by using tleap, >> I found there are some warning in the leap.log file, >> such as: >> -------------------------------------------------------- >> Building proper torsion parameters. >> Building improper torsion parameters. >> ** Warning: No sp2 improper torsion term for C*-CN-CB-CA >> atoms are: CG CE2 CD2 CE3 >> ** Warning: No sp2 improper torsion term for NA-CA-CN-CB >> atoms are: NE1 CZ2 CE2 CD2 > >These are OK: they are torsions about the ring fusion atoms in TRP, and >the force field designer (==me) decided that it was not necessary to have >impropers about these atoms, even though most sp2 atoms do have impropers, >hence the warning when you set your verbosity level up. > >....regards...dac > >-- > >================================================================== >David A. Case | e-mail: >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 | >================================================================== >----------------------------------------------------------------------- >The AMBER Mail Reflector >To post, send mail to >To unsubscribe, send "unsubscribe amber" to >.

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