AMBER Archive (2004)Subject: Re: Re: AMBER: Does this warning matter? (about improper torsion parameters)
From: J. Zhang, Dr (jzhang_at_biophy.nju.edu.cn)
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: 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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