VMD-L Mailing List

From: Anatoly Chernyshev (achernyshev_at_gmail.com)
Date: Mon Nov 05 2018 - 07:13:11 CST

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