VMD-L Mailing List

From: Margaret Shun Cheung (mscheung_at_ipst.umd.edu)
Date: Wed Apr 05 2006 - 20:49:30 CDT

Thank you for the explanation!
Margaret

On Wed, 5 Apr 2006, John Stone wrote:

>
> Hi,
> The psfgen user's guide explains the "poorly guessed coordinate"
> warnings. They are emitted when psfgen guesses coordinates for
> atoms but the topology file doesn't contain lengths or angles them.
> http://www.ks.uiuc.edu/Research/vmd/plugins/psfgen/
>
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Tue, Apr 04, 2006 at 06:17:17PM -0400, Margaret Shun Cheung wrote:
>> Dear VMD wizards,
>>
>> I tried to generate psf from a pdb structure. It gave me warning messages
>> on N-, and C- residues when I run the script:
>>
>> Warning: poorly guessed coordinate for atom HT1 ....
>> Warning: poorly guessed coordinate for atom HT2 ...
>> Warning: poorly guessed coordinate for atom HT3 ..
>> Warning: poorly guessed coordinate for atom OT1 ...
>> Warning: poorly guessed coordinate for atom OT2 ..
>>
>> Can I ignore this warning? Thank you very much.
>> Sincerely,
>>
>>
>> Margaret S. Cheung,
>> Ph. D. Postdoctoral Fellow,
>>
>> ------------------------------------------------------------
>> Room 2117 Tel: (301) 405-4892
>> Inst. for Phys. Sci. & Tech. Fax: (301) 314-9404
>> University of Maryland http://glue.umd.edu/~mscheung
>> College Park, MD 20742-2431 email: mscheung_at_ipst.umd.edu
>> ------------------------------------------------------------
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
>

Margaret S. Cheung,
Ph. D. Postdoctoral Fellow,

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Room 2117 Tel: (301) 405-4892
Inst. for Phys. Sci. & Tech. Fax: (301) 314-9404
University of Maryland http://glue.umd.edu/~mscheung
College Park, MD 20742-2431 email: mscheung_at_ipst.umd.edu
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