Sargis please help with "atom type not found" error

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Sargis please help with "atom type not found" error

Postby sreiling » Mon Jan 13, 2014 10:41 pm

Here is a piece from the dlf for a particular run, I performed.


Institute\AutoDock\4.2.5.1\autodock4.exe: WARNING: the atom type (A) of atom number 34 could not be found;
check that this atom type is listed after the "ligand_types" keyword in the DPF,
and make sure to add a "map" keyword to the DPF for this atom type.
Note that AutoDock will use the default atom type = 1, instead.


I received this error within the dlf, for both "A" type and "N" type. In short, I think I know how to list these atom types in the dpf for the ligand; I just edit with word and add "N" and "A" to the following line:

ligand_types C OA HD # atoms types in ligand

If that is correct, all I need help with, is how to "map" keyword to the DPF for those atom types. How do I do that, and does this involve setting parameters for that particular atom type? Thank you.

ps- I am using PyRx 0.9.1, for what it's worth.
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Re: Sargis please help with "atom type not found" error

Postby sargis » Tue Jan 14, 2014 2:57 am

Thank you for the message. It is not clear how to reproduce this. Could you please create a new ticket using http://sourceforge.net/p/pyrx/tickets/new/ and briefly describe how to reproduce the bug. Please click on Create Account link if you don't have SourceForge.net.

From what I understand, AutoGrid wasn't run before this particular AutoDock run. You can add "map" keyword to the DPF as follow:

Code: Select all
map ../xyz.A.map                      # atom-specific affinity map
map ../xyz.N.map                      # atom-specific affinity map

where xyz is the name of the protein. However, this assumes that AutoGrid created these map files beforehand.

If creating a ticket at SourceForge is too much of a hassle, please repeat the same procedure and see if "N" and "A" are listed under AutoDock Elements on Run AutoGrid page. If so, please click Run AutoGrid button on the lower left and see if that fixes this.

Thank you for using PyRx!
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Re: Sargis please help with "atom type not found" error

Postby sreiling » Tue Jan 14, 2014 7:43 am

Sargis, I would prefer not to open a ticket, if you don't mind bearing with me. However, if you like, I will do so. (You're the boss here, and I am just a student!)

Anyway, I did as you indicated. Actually, I did a bit more. I added the "N" and "A" to my ligand gpf. I will copy&paste a part of the ligand dpf with the alterations I made underlined and bolded:

autodock_parameter_version 4.2 # used by autodock to validate parameter set
outlev 1 # diagnostic output level
intelec # calculate internal electrostatics
seed pid time # seeds for random generator
ligand_types C OA HD N A # atoms types in ligand
fld ..\PDHQL_rigid.maps.fld # grid_data_file
map ..\PDHQL_rigid.C.map # atom-specific affinity map
map ..\PDHQL_rigid.OA.map # atom-specific affinity map
map ..\PDHQL_rigid.HD.map # atom-specific affinity map
map ..\PDHQL_rigid.N.map # atom-specific affinity map
map ..\PDHQL_rigid.A.map # atom-specific affinity map

elecmap ..\PDHQL_rigid.e.map # electrostatics map
desolvmap ..\PDHQL_rigid.d.map # desolvation map
move ..\..\..\Ligands\439351.pdbqt # small molecule
flexres ..\PDHQL_flex.pdbqt # file containing flexible residues


Furthermore, I went into the protein gpf file, and made the following alterations (again, denoted in underline and bold):

npts 50 50 50 # num.grid points in xyz
gridfld PDHQL_rigid.maps.fld # grid_data_file
spacing 0.375 # spacing(A)
receptor_types A C OA N SA HD # receptor atom types
ligand_types C HD OA N A # ligand atom types
receptor PDHQL_rigid.pdbqt # macromolecule
gridcenter -0.74493488715 19.3940204791 22.0800512144 # xyz-coordinates or auto
smooth 0.5 # store minimum energy w/in rad(A)
map PDHQL_rigid.C.map # atom-specific affinity map
map PDHQL_rigid.HD.map # atom-specific affinity map
map PDHQL_rigid.OA.map # atom-specific affinity map
map PDHQL_rigid.N.map # atom-specific affinity map
map PDHQL_rigid.A.map # atom-specific affinity map
elecmap PDHQL_rigid.e.map # electrostatic potential map
dsolvmap PDHQL_rigid.d.map # desolvation potential map
dielectric -0.1465 # <0, AD4 distance-dep.diel;>0, constant

Now, here is the problem: Despite making the above alterations, I still only get three out of the five atom types listed under "Autodock elements", right when I get to the "Run Autogrid" under Autodock Wizard (after I have selected the ligand, and the macromolecule). This is strange for me, because I think I have altered the dpf and gpf files appropriately. Here is the most interesting part.. when I run Autogrid, the alterations I made to the protein.gpf file disappear, and gets rewritten as if I did not make the alterations at all. Further, when I run autodock, in the next step, the alterations made to the ligand.dpf file, also disappear in the same way, and the dpf is rewritten to exclude the alterations.

So, what do you think? Why are the autodock elements not registering the "N" and "A" atom types, and why are the gpf and dpf files being rewritten upon completing the docking simulation, after which I get the exact same errors in the dlf file, which prompted me to start this thread?
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Re: Sargis please help with "atom type not found" error

Postby sargis » Wed Jan 15, 2014 2:11 am

Thank you for the update. Don't worry about opening a ticket. Could you please use PyRx -> Export menu and send me resulting PyRx_workspace.tar.gz file or upload it as an attachment to this topic.

I don't know why it's not registering the "N" and "A" atom types, but if I can get the input files, I'll be able to reproduce this bug and fix it. I'll try to do the following to see if I can reproduce this:
  • start PyRx
  • click on "AutoDock Wizard" tab
  • click Start
  • select Ligand and Macromolecule and click Forward
Please confirm that you still only get three out of the five atom types listed under "Autodock elements" after doing exactly the same steps.

PyRx overwrites the gpf and dpf files before it runs AutoGrid and AutoDock respectively. The only way to avoid this currently is to run AutoGrid and AutoDock outside of PyRx.

I look forward to helping you with this. Please let me know if you have questions or need more information.
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Re: Sargis please help with "atom type not found" error

Postby sreiling » Wed Jan 15, 2014 9:59 pm

Thanks, Sargis! Unfortunately, I must send you the file, directly, since it is too large to attach to this message. I also want to give you a bit more info. After running autogrid, and then starting my autodock 4.2 run, the run will hang. Furthermore, in the progress window for the run, it will give the aforementioned error messages, while hanging. There is one thing I did not realize until now; for some reason the error messages concern atoms that are not in the ligand (despite the messages saying that the atoms ARE in the ligand). For example, there is no ligand atom#19 or 20 or whatnot, but during the run, for some reason AD seems to "think" there is such an atom.

Anyway, I really appreciate your help, and the fact you made PyRx. I look forward to your reply.

edited to add- I sent it to your Scripps email account.
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Re: Sargis please help with "atom type not found" error

Postby sargis » Thu Jan 16, 2014 5:00 am

Thank you for the file. This bug was caused because of the flexible residues. The "N" and "A" atom types are from flexible residues and were not present in the ligand. That's why the error messages concern atoms that are not in the ligand. I have fixed this bug and uploaded updates for this. Please use PyRx -> "Check for Updates..." to apply this update. PyRx would restart and, hopefully, will be able to run AutoDock this time.

Please let me know if you come across other PyRx bugs.

Happy virtual screening!
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Re: Sargis please help with "atom type not found" error

Postby sreiling » Thu Jan 16, 2014 5:00 pm

What a great help, Sargis! It runs fine, now. Thank you! I may actually finish my thesis, this year! :)
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Re: Sargis please help with "atom type not found" error

Postby sreiling » Thu Jan 16, 2014 6:34 pm

Sargis, I hate to tell you this, but after applying the update, I am getting this error, when attempting to use Vina, within PyRx (taken straight from the error log I opted to save):

12:24:02: Error running "D:\Program Files (x86)\PyRx\vina.exe" --config conf.txt --ligand ..\..\Ligands\439351_uff_e=119.11.pdbqt --out "D:\Program Files (x86)\PyRx\Macromolecules\pdhql_flex\439351_uff_e=119.11_out.pdbqt"
12:24:02: Working Directory: D:\Program Files (x86)\PyRx\Macromolecules\pdhql_flex
12:24:02: Stderr: 'D:\Program' is not recognized as an internal or external command,
operable program or batch file.


Please note that Autodock 4.2 works fine, and Vina worked fine before the update. Please let me know, if you need my workspace file, again. Thank you.
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Re: Sargis please help with "atom type not found" error

Postby sargis » Fri Jan 17, 2014 1:36 am

Great, glad to hear AutoDock 4.2 works fine now and sorry about this new issue with Vina.

Vina does run for me for this combination of ligand and macromolecule, although in the end, it doesn't produce any results and I'm getting the following warning:

WARNING: Could not find any conformations completely within the search space.
WARNING: Check that it is large enough for all movable atoms, including those in the flexible side chains.


I tried maximizing the grid box and still no luck. But this is a separate issue.

For the error message you are getting, could you please run Windows Remote Assistance and send me the invitation. I can't think of any other way to reproduce this error now but to run Remote Desktop Connection.

Thank you much!
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Re: Sargis please help with "atom type not found" error

Postby mwells » Mon Jun 30, 2014 3:54 pm

Hi Sargis,

in a similar vein to sreiling: I have ~ 1000 compounds containing boron and silicon - is there any way to transform these into screenable compounds?

Kind Regards,

Mike
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