Re: [apbs-users] WARNING: Duplicate atom names (C) found in ligand file ...
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Re: [apbs-users] WARNING: Duplicate atom names (C) found in ligand file ...
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From: Baker, N. <Nat...@pn...> - 2012-05-19 18:25:54
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Hi Francois -- Kyle, Cc'ed above, is looking into this issue. Thanks, __________________________________________________ Nathan Baker Pacific Northwest National Laboratory Tel: +1-509-375-3997 http://nabaker.me -----Original Message----- From: Francois Berenger [mailto:ber...@ri...] Sent: Thursday, May 17, 2012 5:27 PM To: apb...@li... Subject: Re: [apbs-users] WARNING: Duplicate atom names (C) found in ligand file ... On 05/17/2012 10:49 AM, Francois Berenger wrote: > Hello, > > --- > WARNING: Duplicate atom names (C) found in ligand file, please change > duplicate atom names to aviod atom overwriting! > --- > > This problem could be easily avoided if pdb2pqr uses > atom_number:atom_name read in the mol2 file instead of just the > atom_name as a unique identifier. In fact, this is a bug: some mol2 file with obviously same format work while others produce the above-mentioned warning. replacing atom_names with atom_name_atom_number (like C to C1 then next C to C2) does remove the warning but there may be a more subtle bug involved. > Regards, > F. > > ------------------------------------------------------------------------------ > 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 ------------------------------------------------------------------------------ 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 |