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

From: J. Zhang, Dr <jzhang.biophy.nju.edu.cn>
Date: Thu, 20 May 2004 9:57:35 +0800

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.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 May 20 2004 - 03:53:01 PDT
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