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Electrostatics / apbs-pdb2pqr

APBS - software for biomolecular electrostatics and solvation
http://www.poissonboltzmann.org/
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getting UHBD potential from pdb #532

Closed mwscandura closed 4 years ago

mwscandura commented 4 years ago

multi-part issue here. New to the software, trying to make an automated script for inputting pdb files and outputting UHBD grids.

general workflow for what I'm stuck on is

  1. invoke pdb2pqr to create a subA.pqr file w/o water and w/ proper protonation, and create ABPS input file pdb2pqr --ff=amber --chain --drop-water --verbose --apbs-input --ph-calc-method=propka --with-ph=7.4 --propka-verbose $COREDIR/input/subA.pdb $WORKDIR/pdb2pqrA/subA.pqr outputs subA.pqr and subA.in

  2. make APBS of PQR file w/ electrostatic potential grids using APBS input file apbs subA.in outputs subA.pqr.dx

the issue is that i need the output to be in UHBD format, not OPENDX

I've scoured the documentation and see that UHBD is a supported output format (section 8.1.3) but don't understand how to do this. I understand that in the ABPS input file ELEC section, the line write pot dx can be changed to write pot uhbd, but doing this manually i get this: Vgrid_writeUHBD: can't write UHBD mesh with non-uniform spacing

SO, short version of the question is how do i generate a UHBD output starting from a PDB? Longer version is:

kozlac commented 4 years ago

Hello @mwscandura, if you look at the contents of the subA.in file you should see the cglen and fglen keywords. In order for APBS to output the potential map in UHBD format these (x,y,z) values should be the same in each direction (Hence the non-uniform error). The cglen dimensions should be large enough to encompass the entire molecule while the fglen ones should cover the area of interest. Please see this link for a description of the keywords.

There's no PDB2PQR step to automatically write the in file to write in UHBD format. You could write a python script to take the max in each of the cglen and fglen, make them uniform, and change the write line. Please let me know if you need help with that.

mwscandura commented 4 years ago

I see. Any help or guidance on writing the python script would be excellent, I'm not familiar with the langauge

kozlac commented 4 years ago

Hello @mwscandura, the following script will take all the .in files in a folder an change the cglen and fglen to the corresponding max's and change the write format to uhbd as long as you have python 3.5 or higher installed. For example in an Ubuntu system just put the script in the same folder as all the .in files and run: python3 convert2uhbd.py.

convert2uhbd.zip

Let me know if you have any troubles. Thanks!!

mwscandura commented 4 years ago

Thanks again for this, Juan. I’ve only just had a chance to take a look and try to get it working with what I’m doing. It didn’t seem to go through in my first attempt and I got a few error messages back that maybe you can clear up:

line 6: import: command not found line 8: syntax error near unexpected token (' line 8:def getMax(l):'

I’m running python 3.7.3

EDIT: never mind, got it all to run smoothly. was missing a couple things on my end. thanks again!

Matthew Scandura Postbaccalaureate Fellow, IRTA Laboratory of Immune System Biology (LISB) National Instittue of Allegy & Infectious Diseases (NIAID) National Institutes of Health (NIH), HHS

From: Juan notifications@github.com Sent: Monday, December 2, 2019 1:31 PM To: Electrostatics/apbs-pdb2pqr apbs-pdb2pqr@noreply.github.com Cc: Scandura, Matthew (NIH/NIAID) [F] matthew.scandura@nih.gov; Mention mention@noreply.github.com Subject: Re: [Electrostatics/apbs-pdb2pqr] getting UHBD potential from pdb (#532)

Hello @mwscandurahttps://github.com/mwscandura, the following script will take all the .in files in a folder an change the cglen and fglen to the corresponding max's and change the write format to uhbd as long as you have python 3.5 or higher installed. For example in an Ubuntu system just put the script in the same folder as all the .in files and run: python3 convert2uhbd.py.

convert2uhbd.ziphttps://github.com/Electrostatics/apbs-pdb2pqr/files/3912746/convert2uhbd.zip

Let me know if you have any troubles. Thanks!!

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/Electrostatics/apbs-pdb2pqr/issues/532?email_source=notifications&email_token=AN2SBR3VYQYAQL5OY5DD42TQWVH7FA5CNFSM4JRPFPWKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEFUOEDI#issuecomment-560521741, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AN2SBR2OSPI6MFZ4PPZQKATQWVH7FANCNFSM4JRPFPWA.

kozlac commented 4 years ago

Marking it as resolved.

mwscandura commented 4 years ago

Hello Juan,

I’m unsure if you’ll still see replies in response to this. We corresponded over Github a few months ago regarding an issue with outputting UHBD formatted files in APBS. Thanks again for the script. I made a small modification (turns out the dime also have to all be equal) and I’ve integrated it into my pipeline. I’m a researcher at the NIH this pipeline is a major part of my project, which I’ll be presenting to my lab group about next week. I’d like to include you in the acknowledgments and wanted to ask how to most appropriately do so.

Thanks, Matthew

Matthew Scandura Postbaccalaureate Fellow, IRTA Laboratory of Immune System Biology (LISB) National Institute of Allergy & Infectious Diseases (NIAID) National Institutes of Health (NIH), HHS

From: Juan notifications@github.com Sent: Monday, December 2, 2019 1:31 PM To: Electrostatics/apbs-pdb2pqr apbs-pdb2pqr@noreply.github.com Cc: Scandura, Matthew (NIH/NIAID) [F] matthew.scandura@nih.gov; Mention mention@noreply.github.com Subject: Re: [Electrostatics/apbs-pdb2pqr] getting UHBD potential from pdb (#532)

Hello @mwscandurahttps://github.com/mwscandura, the following script will take all the .in files in a folder an change the cglen and fglen to the corresponding max's and change the write format to uhbd as long as you have python 3.5 or higher installed. For example in an Ubuntu system just put the script in the same folder as all the .in files and run: python3 convert2uhbd.py.

convert2uhbd.ziphttps://github.com/Electrostatics/apbs-pdb2pqr/files/3912746/convert2uhbd.zip

Let me know if you have any troubles. Thanks!!

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/Electrostatics/apbs-pdb2pqr/issues/532?email_source=notifications&email_token=AN2SBR3VYQYAQL5OY5DD42TQWVH7FA5CNFSM4JRPFPWKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEFUOEDI#issuecomment-560521741, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AN2SBR2OSPI6MFZ4PPZQKATQWVH7FANCNFSM4JRPFPWA.

kozlac commented 4 years ago

Hello @mwscandura. I'm really glad I was able to help. I think Juan Brandi, Computer Scientist with the APBS development team would do. Thanks!!

mwscandura commented 4 years ago

Will do!

Matthew Scandura Postbaccalaureate Fellow, IRTA Laboratory of Immune System Biology (LISB) National Institute of Allergy & Infectious Diseases (NIAID) National Institutes of Health (NIH), HHS

From: Juan notifications@github.com Sent: Wednesday, February 12, 2020 7:15 PM To: Electrostatics/apbs-pdb2pqr apbs-pdb2pqr@noreply.github.com Cc: Scandura, Matthew (NIH/NIAID) [F] matthew.scandura@nih.gov; Mention mention@noreply.github.com Subject: Re: [Electrostatics/apbs-pdb2pqr] getting UHBD potential from pdb (#532)

Hello @mwscandurahttps://github.com/mwscandura. I'm really glad I was able to help. I think Juan Brandi, Computer Scientist with the APBS development team would do. Thanks!!

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/Electrostatics/apbs-pdb2pqr/issues/532?email_source=notifications&email_token=AN2SBRYQSNSJV2VW2BORUT3RCSGJ5A5CNFSM4JRPFPWKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOELS4M3I#issuecomment-585483885, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AN2SBR3PY4LXTCKGQHCMXEDRCSGJ5ANCNFSM4JRPFPWA.