VMD-L Mailing List

From: João Ribeiro (jribeiro_at_ks.uiuc.edu)
Date: Mon Nov 12 2018 - 10:27:28 CST

Hi Anatoly,

Sorry for the late reply. Can you please check in the terminal window
of VMD, before the "Molecule destroyed" message, if there is any other
meaningful error message? Another question is which version of VMD are
you using? 1.9.4? Make sure that you reset QwikMD after adding the str
file.

Best

João
On Mon, Nov 5, 2018 at 7:13 AM Anatoly Chernyshev <achernyshev_at_gmail.com> wrote:
>
> Hello all. Possibly a kindergardenish question... I was trying to test-run 2AVI protein (avidin protein complexed with biotin) in QuickMD. To parametrize biotin, I cut out its lines from the pdb file, added hydrogens in Avogadro, converted to mol2, and finally got the rtf and prm files from CGEnFF.
>
> When I put the 2AVI file in QuickMD, I've added these parameter files, and the system was happy and not complaining about the new BTN hetero moiety.
>
> Now, when I click "Prepare" there's the "Molecule destroyed" error from psfgen, telling me that the BTN residue is not recognised (although it's clearly marked as 'hetero' type).
>
> What I might be doing wrong?
>
> TIA 

-- 
……………………………………………………...
João Vieira Ribeiro
Theoretical and Computational Biophysics Group
Beckman Institute, University of Illinois
http://www.ks.uiuc.edu/~jribeiro/
jribeiro_at_ks.uiuc.edu
+1 (217) 3005851