VMD-L Mailing List

From: Arneh Babakhani (ababakha_at_mccammon.ucsd.edu)
Date: Fri Jul 20 2007 - 12:35:24 CDT

Ok, thanks, yes I do think it would be useful, what's the process of
writing a plugin? what do you have to code in?
>
> Arneh,
> We don't have a reader for Autodock's "pdbqt" format, but if
> a lot of people would find it very useful to be able to load them
> a pdbqt plugin could be written. Even better, if someone familiar
> with pdbqt wants to write the plugin, I can give guidance and help
> them get it done... :-)
>
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Thu, Jul 19, 2007 at 04:01:01PM -0700, Arneh Babakhani wrote:
>> Hi,
>>
>> I have a pdb file, that I convert to a pdbqt using AutoDock.
>>
>> I'm trying to read in this pdbqt file into VMD. (at the command line,
>> I'm
>> just entering 'vmd Molecule.pdbqt').
>>
>> But VMD isn't displaying the entire molecule (is it confused by the
>> 'BRANCH' line in the pdbqt???).
>>
>> I've pasted the pdbqt below, and attached the files.
>>
>> Thanks,
>>
>> Arneh
>>
>>
>> REMARK 1 active torsions:
>> REMARK status: ('A' for Active; 'I' for Inactive)
>> REMARK 1 A between atoms: A5_3 and C1_8
>> ROOT
>> ATOM 1 C1 EPA 2 -3.086 0.090 1.171 1.00 0.00
>> 0.052
>> ATOM 2 C3 EPA 2 -3.033 0.853 2.533 1.00 0.00
>> 0.195
>> ATOM 3 N5 EPA 2 -2.941 -0.245 3.498 1.00 0.00
>> -0.066
>> ATOM 4 H6 EPA 2 -2.123 -0.836 3.333 1.00 0.00
>> 0.278
>> ATOM 5 H7 EPA 2 -2.985 0.088 4.464 1.00 0.00
>> 0.278
>> ATOM 6 C8 EPA 2 -4.398 1.477 2.926 1.00 0.00
>> 0.036
>> ATOM 7 C11 EPA 2 -5.220 0.225 3.307 1.00 0.00
>> 0.035
>> ATOM 8 C14 EPA 2 -4.182 -0.902 3.087 1.00 0.00
>> 0.187
>> ATOM 9 C16 EPA 2 -3.904 -1.169 1.587 1.00 0.00
>> 0.044
>> ENDROOT
>> BRANCH 1 10
>> ATOM 10 A5 EPA 1 -1.797 -0.269 0.494 1.00 0.00
>> -0.034
>> ATOM 11 A3 EPA 1 -1.838 -0.771 -0.830 1.00 0.00
>> 0.012
>> ATOM 12 A7 EPA 1 -0.520 -0.156 1.096 1.00 0.00
>> 0.126
>> ATOM 13 A1 EPA 1 -0.659 -1.121 -1.513 1.00 0.00
>> 0.045
>> ATOM 14 A11 EPA 1 0.574 -0.972 -0.856 1.00 0.00
>> 0.125
>> ATOM 15 c EPA 1 2.028 -1.371 -1.619 1.00 0.00
>> -0.062
>> ATOM 16 N9 EPA 1 0.602 -0.501 0.415 1.00 0.00
>> -0.248
>> ENDBRANCH 1 10
>> TORSDOF 1
>
>
>
>
> --
> 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
>