Too many atom types!

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Too many atom types!

Postby wazeer » Thu Jul 10, 2014 5:59 pm

Hi Sargis,

I have run Vina successfully but when I tried using Autodock4 with the NCI library, it gives me "Too many atom types" error although each ligand by itself does not have more than 12 different atom types, please let me know what to do about that ?

Thanks,

Muhamad
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Re: Too many atom types!

Postby sargis » Sat Jul 12, 2014 12:04 am

Hi Muhamad,

Thank you for the message. Glad to hear you have run Vina successfully. For Autodock4, try doing first half of NCI library first, then the second half.

Thank you for using PyRx!
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Re: Too many atom types!

Postby wazeer » Sat Jul 12, 2014 12:08 am

Thanks for your reply, I already did that but still the same error persists! Also if I select a subset of the ligands, I get another error - unknown atom type *atotype.

Also can you make the ligands tool capable to search subfolders, I have added two subfolders in .PyRx_workspace/Ligands containing different sets of ligands but when running AutoDock vina, it did not manage to see them - it only sees the ligands at the Lignads folder but not the subfolders,

Thanks for your help,

Muhammad
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Re: Too many atom types!

Postby sargis » Sat Jul 12, 2014 12:21 am

wazeer wrote:Thanks for your reply, I already did that but still the same error persists! Also if I select a subset of the ligands, I get another error - unknown atom type *atotype.

You are welcome. Maybe it's worth tracking down which ligands give unknown atom type *atotype. If you can upload these ligands here, I can try to track it down and see what's going on.
wazeer wrote:Also can you make the ligands tool capable to search subfolders, I have added two subfolders in .PyRx_workspace/Ligands containing different sets of ligands but when running AutoDock vina, it did not manage to see them - it only sees the ligands at the Lignads folder but not the subfolders,

Great idea. I'll think about implementing this in the next release.
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Re: Too many atom types!

Postby wazeer » Sat Jul 12, 2014 12:25 am

That is the funny thing here that all those ligands do not have too many atoms, if you run just one ligand by itself, autodock runs fine but if you select like 60 ligands it gives you either too many atom types or unknown *atotype atom type. None of those ligands contain unknown atom type and also I did use them with Vina and everything run smoothly!
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Re: Too many atom types!

Postby wazeer » Thu Jul 17, 2014 11:00 am

Finally I found the fixing. This error is originating from autodock4, when it generates the dpf file, the lines containing the map files are written like that ->
map ../1be3_cytob_phyd_bs_2_phyd_nohem_rigid.A.map# atom-specific affinity map, so it searches for this file and will not find it because of #. And if you modify the map files and add # to their name, you will get "Too many atom types" or uknown atom type "atotype". So the fix is that you have to modify two lines in the DockingParameters.py file in PyRx-0.9.2/lib64/python2.6/site-packages/AutoDockTools, as follows,

self['fld']['value'] = self.receptor_stem + '.maps.fld '

val_str = self.receptor_stem + ".%s.map " % (type)

mol_types = mol_types + " " + t + " "

Notice the space after .fld and after .map,

This will fix things up,

Good luck for all,

Muhammad
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Re: Too many atom types!

Postby sargis » Thu Jul 17, 2014 12:19 pm

Good find! Thank you very much. I'll try to include this in the next release of PyRx.
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Re: Too many atom types!

Postby wazeer » Thu Jul 17, 2014 7:49 pm

Thanks Sargis, but there is still one problem, the atoms line -> ligand_types A C Cl I NA F OA N P S Br SA HD# atoms types in ligand, is still incorrect
because # is next to HD and no space between them, can you tell me which line in DockingParameters.py should I modify ? I tried several lines but nothing works!
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Re: Too many atom types!

Postby wazeer » Thu Jul 17, 2014 9:02 pm

Actually all what we have to change this line only,

return "%s %s%s # %s\n" % (p['keyword'],

There is now a space before #. Now everything works smooth,

Thanks,

Muhammad
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Re: Too many atom types!

Postby sargis » Thu Jul 17, 2014 10:51 pm

Thank you very much. This will be great help for users who encounter this issue.
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