No heavy atoms found for RNA coordinates

Electrostatics / apbs-pdb2pqr

APBS - software for biomolecular electrostatics and solvation

http://www.poissonboltzmann.org/

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No heavy atoms found for RNA coordinates #506

Closed chenzhao-CZ closed 4 years ago

chenzhao-CZ commented 7 years ago

I have encountered problems when I tried to generate pqr file for APBS using AMBER force filed on a RNA molecule. The error message is something like no heavy atoms found. However, the coordinates is just a regular RNA molecule that is consistent with AMBER naming scheme. What should I try to solve this problem?

kozlac commented 7 years ago

Hello @chenzhao-CZ, could you tell us what if you are using PDB2PQR (server or local install, if local what version?) and maybe share with us the pdb file you are using?

chenzhao-CZ commented 7 years ago

Sorry for the delayed reply as I was traveling the last weekend. I have PDB2PQR version 2.1.1 on a local machine. The PDB file has PDBID 4FAQ. Thank you very much!

speleo3 commented 6 years ago

For RNA the residue names need to be change to RA, RC, RG, and RU

See https://sourceforge.net/p/pdb2pqr/mailman/message/33298335/