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Re: [apbs-users] Simple question
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From: Baker, N. <Nat...@pn...> - 2012-08-07 20:20:12
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Hello -- Did you assign titration states using PDB2PQR for both models? Thanks, __________________________________________________ Nathan Baker Pacific Northwest National Laboratory Tel: +1-509-375-3997 http://nabaker.me -----Original Message----- From: Michael Osborne [mailto:mic...@um...] Sent: Tuesday, August 07, 2012 9:04 AM To: apb...@li... Subject: [apbs-users] Simple question Hi everyone I have a simple question about the electrostatics calculations: I have been running apbs calculations via the pdb2pqr server to get he pqr and .dx files. I have two very similar proteins: but their electrostatics potentials look very different: in particular I have noticed that in one of the calculation the Trp ring have a -ve charge - whilst in the other it is pretty much neutral. The one difference is that one structure is calculated from NMR (xplor) so had H atoms. The other is an Xray structure.. however for both I used pdb2pqr, so this should not make a difference and all other paramters for calculations are the same. Am I doing something wrong? Thanks in advance for any help Cheers Mike ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ apbs-users mailing list apb...@li... https://lists.sourceforge.net/lists/listinfo/apbs-users |