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 Post subject: molybdenum
PostPosted: Sat Jul 11, 2009 8:27 pm 
Millimolar User
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Joined: Sat Jul 11, 2009 8:03 pm
Posts: 8

first of all, i must congratulate Oleg for the excellent software Vina.

i have got few queries:

firstly, i have been trying to dock against my protein that contains molibdenum as a cofactor and i must include it. now during running, Vina gave me the message ''Parse error in on line 7069 in file 1fiq.pdbqt: ATOM syntax is incorrect: Mo is not a valid AutoDock type''. How can i correct for this problem?

secondly, few users have used water molecules in the protein. and the type of proteins that i am working with, most of them require some critical water molecules which are known to form hydrogen bonding with the ligands. Do you recommend any standard procedure for the inclusion of water molecules?

in some cases, i found that Vina places the ligand almost exactly in its original position in the crystal structure but the orientation of the docked ligand gets totally reversed (it becomes, say 'back to front' compared to 'front to back' of the orginal pose). for example, i have been trying to redock Harmine to human MAO-A (PDB 2z5x) but having this orientation reversing problem often (see the conf text parameters below). i tried with lowering the GRID size but the problem still remains. do you have any advice on this?

center_x = 39.133
center_y = 31.12
center_z = -15.347

size_x = 35
size_y = 45
size_z = 45

thirdly, do you recommend energy minimizing the ligand molecule using a different software before running in Vina? it seems some people are doing it. but i thought Vina takes care of it during docking anyway. am i right?

thanks again for developing Vina. its really great to use.


Last edited by oleg_trott on Thu Jul 16, 2009 11:39 pm, edited 1 time in total.
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 Post subject: Re: few queries
PostPosted: Thu Jul 16, 2009 11:12 pm 
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Joined: Mon Oct 20, 2008 9:39 pm
Posts: 202

Transition metals are not supported at this time. If you'd like to get some answer out of Vina rather than none, you may want to try replacing molybdenum with a common metal (that Vina knows about).

Regarding the "reversing" problem. For some receptor-ligand complexes, the scoring function will identify the wrong conformation as "more preferable" (see the paper). If that is the problem, there is not much you can do about that. A different scoring function might do better on that complex and worse on another.

If you don't get your question answered here, consider posting it on the AutoDock mailing list instead of this forum. Please do not email or PM me with requests for help.

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