[Dock-fans] Problem with the DOCK 6.2 solvent_scoring_demo

[Vidana.Epa at csiro.au]

Hi Scott,

	The parameters file prot.table.ambcrg.ambH (and this is also the case with the one in the chemgrid subdirectory) denotes, for example, the amide hydrogen as 'HN' while rec.pdb calls it 'H', and so on. Instead of prot.table.ambcrg.ambH, INCHEM should call for prot.table.ambcrg.pdbH, AFTER first changing the Lys protons from '1HZ1', '2HZ1', '3HZ1' (as they are in prot.table.ambcrg.pdbH right now) to 'HZ1', 'HZ2', 'HZ3'. This fixes the problem, in so far as now you get an integer total charge (-2.0). Note however, the 'HIS' residues in rec.pdb are positively charged, (I would normally keep His neutral unless there was a specific reason to charge them, and then I would use the Amber notation of calling them 'HIP'), and the N-terminus is neutral while the C-terminus carries a -1.0 charge (probably won't affect the scoring, but just niggling inconsistencies).

Cheers,

Vidana.



Vidana C. Epa
 
CSIRO,
Division of Molecular Health & Technologies,
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Parkville, Victoria 3052,
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email: Vidana.Epa at csiro.au
-----Original Message-----
From: Scott Brozell [mailto:sbrozell at rci.rutgers.edu] 
Sent: Saturday, 11 April 2009 4:43 AM
To: Epa, Vidana (CMHT, Parkville)
Cc: dock-fans at docking.org
Subject: Re: [Dock-fans] Problem with the DOCK 6.2 solvent_scoring_demo

Hi,

On Fri, 10 Apr 2009, Vidana.Epa at csiro.au wrote:

>            Running the solvent_scoring_demo (in the Dock 6.2 distribution tutorials section), it appears from the grid output file "OUTPARM" (in /solvent_scoring_demo/3_grid/nchemgrid_GB/), a non-integer total charge is computed for the rec.pdb (-144.488, in fact). This arises from the incompatibility of the hydrogen atom format in rec.pdb with that of the parameter file prot.table.ambcrg.ambH. Shouldn't this be corrected?
>

I do not know.  We'll add this to the to-do list.
Can you send more details?
Have you tried parameters/chemgrid/prot.table.ambcrg.ambH ?

Thanks for the report.
Scott