ADL: Problems with vina - invalid atom type

classic Classic list List threaded Threaded
2 messages Options
Reply | Threaded
Open this post in threaded view
|

ADL: Problems with vina - invalid atom type

Fok Mello
Hi!

I'm trying to dock 1vnc.pdb with hydrogen peroxide.pdb as my beginner's task using VINA

when i run the vina the cmd said the vanadium (V) atom in 1vnc.pdb is not a valid autodock type.

I looked forward in the forum and it seems that elements with two characteristics such as "Mo" "Hb" "Ho" share the similar problems.
Correcting the pdbqt file manually would be the solution.

However, the very syntax about the vanadium in the pdbqt file is O.K.

How shall I proceed than? Please Help!

Many thanks!

Bests,

Mello

________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
Reply | Threaded
Open this post in threaded view
|

Re: ADL: Problems with vina - invalid atom type

Diogo Martins
Hello,

Vanadium is not supported.

You can rename it to a supported metal, such as iron or zinc.

Best,




On Oct 19, 2017 4:38 AM, "Fok Mello" <[hidden email]> wrote:

Hi!

I'm trying to dock 1vnc.pdb with hydrogen peroxide.pdb as my beginner's
task using VINA

when i run the vina the cmd said the vanadium (V) atom in 1vnc.pdb is not a
valid autodock type.

I looked forward in the forum and it seems that elements with two
characteristics such as "Mo" "Hb" "Ho" share the similar problems.
Correcting the pdbqt file manually would be the solution.

However, the very syntax about the vanadium in the pdbqt file is O.K.

How shall I proceed than? Please Help!

Many thanks!

Bests,

Mello

________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---