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Electrostatics / apbs-pdb2pqr

APBS - software for biomolecular electrostatics and solvation
http://www.poissonboltzmann.org/
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Error message that I have no idea how to fix #509

Closed skigirl618 closed 6 years ago

skigirl618 commented 6 years ago

I am trying to run a PQR file I made in pdb2pqr through apbs and I keep getting this error message: Vcom_ctor2: process 0 of 1 is ALIVE! Valist_readPQR: Error parsing atom 4111! Please double check this atom in the pqr file, e.g., make sure there are no concatenated fields. Error reading molecules!

I am not good with code at all so I have no idea how to fix this or if it is an issue with the original PDB.

kozlac commented 6 years ago

Hello @skigirl618, it seems that the issue is in the pqr file that is being provided to APBS. You can open the pqr file with any text editor and go to atom 4111 and make sure that it follows the right format (i.e. compare it to the other atoms that are being read correctly. Most likely, one of the values has more significant digits and is running into the next one. You should be able to separate them by spaces. Also, please feel free to email me your pqr file (juan.brandi-lozano@pnnl.gov) and I could check it too.

kozlac commented 6 years ago

The problem was some of the (x, y, z) values for the ATOM records in the pqr file were concatenated, e.g.:

ATOM 1234 AB ABC 123 53.070 30.252-100.167 -0.0000 1.0000

The solution is to make sure there is a space between them:

ATOM 1234 AB ABC 123 53.070 30.252 -100.167 -0.0000 1.0000