Dear users and developers,
I am using AMBER 10 on ubuntu 10.04 LTS. I
generated my 10mer pdb
(nuc.pdb) from Tutorial B1. when I try to load this pdb leap adds 122
atoms to it.
The pdb, as per tutorial must contain 638 atoms and no atom further
added.
Following is the output that appears on xleap.
Created a new atom named: H5'' within residue: .R<DT 16>
Created a new atom named: H2' within residue: .R<DT 16>
Created a new atom named: H2'' within residue: .R<DT 16>
Added missing heavy atom: .R<DT 16>.A<O1P 2>
Added missing heavy atom: .R<DT 16>.A<O2P 3>
Created a new atom named: OP1 within residue: .R<DT 17>
Created a new atom named: OP2 within residue: .R<DT 17>
Created a new atom named: H5' within residue: .R<DT 17>
Created a new atom named: H5'' within residue: .R<DT 17>
Created a new atom named: H2' within residue: .R<DT 17>
Created a new atom named: H2'' within residue: .R<DT 17>
Added missing heavy atom: .R<DT 17>.A<O1P 2>
Added missing heavy atom: .R<DT 17>.A<O2P 3>
Created a new atom named: OP1 within residue: .R<DT 18>
Created a new atom named: OP2 within residue: .R<DT 18>
Created a new atom named: H5' within residue: .R<DT 18>
Created a new atom named: H5'' within residue: .R<DT 18>
Created a new atom named: H2' within residue: .R<DT 18>
Created a new atom named: H2'' within residue: .R<DT 18>
Added missing heavy atom: .R<DT 18>.A<O1P 2>
Added missing heavy atom: .R<DT 18>.A<O2P 3>
Created a new atom named: OP1 within residue: .R<DT 19>
Created a new atom named: OP2 within residue: .R<DT 19>
Created a new atom named: H5' within residue: .R<DT 19>
Created a new atom named: H5'' within residue: .R<DT 19>
Created a new atom named: H2' within residue: .R<DT 19>
Created a new atom named: H2'' within residue: .R<DT 19>
Added missing heavy atom: .R<DT 19>.A<O1P 2>
Added missing heavy atom: .R<DT 19>.A<O2P 3>
Created a new atom named: OP1 within residue: .R<DT 20>
Created a new atom named: OP2 within residue: .R<DT 20>
Created a new atom named: H5' within residue: .R<DT 20>
Created a new atom named: H5'' within residue: .R<DT 20>
Created a new atom named: H2' within residue: .R<DT 20>
Created a new atom named: H2'' within residue: .R<DT 20>
Created a new atom named: HO3' within residue: .R<DT 20>
Added missing heavy atom: .R<DT 20>.A<O1P 2>
Added missing heavy atom: .R<DT 20>.A<O2P 3>
total atoms in file: 638
Leap added 122 missing atoms according to residue templates:
42 Heavy
80 H / lone pairs
--
Chirag V. Vora <chiragvora.live.com>
Department of Pharmacoinformatics <http://pharmacoinformatics.tripod.com/>,
National Institute of Pharmaceutical Education and Research<http://niper.ac.in>
*Sector 67, S.A.S. Nagar, *
*Punjab (INDIA) - 160 062, *
*Phone: +91-9814187740*
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Received on Wed Jun 29 2011 - 23:00:04 PDT
