Re: [Pdb2pqr-users] PDB2PQR failure to rename C-terminal CYS to CYX

[Baker, N. <Nat...@pn...>]

Hi Matias –

I’m Cc’ing Kyle Monson and Liz Jurrus for their help with this.

Thanks,

--
Nathan Baker
Laboratory Fellow
Computational and Statistical Analytics Division
Pacific Northwest National Laboratory
+1-509-375-3997
https://goo.gl/H3X8f1

From: Matias Machado [mailto:mat...@gm...]
Sent: Monday, September 14, 2015 12:08 PM
To: pdb...@li...
Subject: [Pdb2pqr-users] PDB2PQR failure to rename C-terminal CYS to CYX

Dear APBS developers,

I may have found a bug in the pdb2pqr 2.0.0 release.

When processing the PDB id 1ETM either with the server or the standalone version, pdb2pqr fails to correctly rename the C-terminal CYS 17 residue to CYX. However this Cysteine is PATCHED to CYX as reported in the stdout.

Any guess why?

This is the command line:
pdb2pqr --ff=amber --ffout=amber --with-ph=7 --chain 1ETM.pdb 1ETM.pqr
Thanks for your answer!

Best regards,

Matías Machado