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Electrostatics / apbs

Software for biomolecular electrostatics and solvation calculations
http://www.poissonboltzmann.org/
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psize.py #136

Open sbembenek18 opened 3 years ago

sbembenek18 commented 3 years ago

When using psize.py with my PQR file (psize.py myfile.pqr) it gives:

No ATOM entires in file!

However, when I use the Pymol plugin with the same PQR and the .mol to match, it works just fine.

And when APBS using the same PQR file (after the cglen & fglen have been set in the input file manually), it works fine as well.

It appears the error is because the PQR is for a small molecule (not a protein) and, as such, only has HETATM declarations. Nonetheless, I'm not sure how to proceed.

Also, do I correctly understand that the input file values, cglen and fglen are usually calculated by psize.py and that you do need these values in your input file prior to running APBS. In other words, APBS does not call psize.py during run time -- correct?

thanks!

Scott

sobolevnrm commented 3 years ago

Hi --

Much of the psize.py functionality has been integrated into pdb2pqr; we are planning to deprecate the psize.py tool provided with APBS. Have you tried PDB2PQR?

Thanks,

Nathan

sbembenek18 commented 3 years ago

Will do -- thanks!

sbembenek18 commented 3 years ago

Unfortunately, I am unable to generate a PQR for the ligand. I'm using the command:

pdb2pqr30 --ff=PARSE --ligand=frag.mol2 frag.pdb out.pqr

I actually have a pqr file that works with APBS -- I'm really looking for a way to generate a (new) input for APBS and get parameter suggestion therein. However -- as noted -- psize isn't working with my current PQR, so I am not sure how to get the info in an automated fashion otherwise (other than going through the Pymol Plugin).

I've attached the files.

thanks for the help!

frag.mol2.txt frag.pdb.txt