PDB2PQR generates misaligned residue names for GLU (and possibly others)
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sobolevnrm commented
It appears that lines like this are causing the problem:
ATOM 855 OE1GLUP 54 12.441 4.942 -21.757 -0.5500 1.7000
ATOM 856 OE2GLUP 54 13.699 6.052 -23.197 -0.6100 1.7700
The protonated glutamate residue name is misaligned. I've realigned them in the attached file and it seems to work fine. Could you please provide the input PDB that generated this problem?
Thank you.
Originally posted by @sobolevnrm in Electrostatics/apbs#265 (comment)