[AMBER] Error while running tleap in AMBER

From: Shreeramesh <shreeramesh.gmail.com>
Date: Thu, 15 Jan 2015 05:08:05 -0800

Dear all,

I ran a tleap using pdb file and I got a following error. Can you please
suggest to solve the following error. I also attached the script for tleap
and pbd of protein for your kind attention.


Loading PDB file: ./rec.pdb
-- residue 333: duplicate [ C] atoms (total 2)
-- residue 333: duplicate [ CA] atoms (total 2)
-- residue 333: duplicate [ N] atoms (total 2)
-- residue 333: duplicate [ O] atoms (total 2)
-- residue 334: duplicate [ C] atoms (total 2)
-- residue 334: duplicate [ CA] atoms (total 2)
-- residue 334: duplicate [ CB] atoms (total 2)
-- residue 334: duplicate [ N] atoms (total 2)
-- residue 334: duplicate [ O] atoms (total 2)
-- residue 177: duplicate [ C] atoms (total 2)
-- residue 177: duplicate [ CA] atoms (total 2)
-- residue 177: duplicate [ CB] atoms (total 2)
-- residue 177: duplicate [ CG] atoms (total 2)
-- residue 177: duplicate [ N] atoms (total 2)
-- residue 177: duplicate [ O] atoms (total 2)
-- residue 177: duplicate [ OD1] atoms (total 2)
-- residue 177: duplicate [ OD2] atoms (total 2)
-- residue 204: duplicate [ C] atoms (total 2)
-- residue 204: duplicate [ CA] atoms (total 2)
-- residue 204: duplicate [ CB] atoms (total 2)
-- residue 204: duplicate [ CD] atoms (total 2)
-- residue 204: duplicate [ CG] atoms (total 2)
-- residue 204: duplicate [ N] atoms (total 2)
-- residue 204: duplicate [ O] atoms (total 2)
-- residue 204: duplicate [ OE1] atoms (total 2)
-- residue 204: duplicate [ OE2] atoms (total 2)
-- residue 478: duplicate [ CA] atoms (total 2)
-- residue 478: duplicate [ CB] atoms (total 2)
-- residue 478: duplicate [ CD] atoms (total 2)
-- residue 478: duplicate [ CG] atoms (total 2)
-- residue 478: duplicate [ OE1] atoms (total 2)
-- residue 478: duplicate [ OE2] atoms (total 2)

Warning: Atom names in each residue should be unique.
     (Same-name atoms are handled by using the first
      occurrence and by ignoring the rest.
      Frequently duplicate atom names stem from alternate
      conformations in the PDB file.)

Unknown residue: ASN number: 0 type: Terminal/beginning
..relaxing end constraints to try for a dbase match
  -no luck
Unknown residue: SER number: 1 type: Nonterminal
Unknown residue: PRO number: 2 type: Nonterminal
Unknown residue: ILE number: 3 type: Nonterminal
........
........
........etc.....

Thanks & regards

*Ramesh M*
Email: shreeramesh.gmail.com


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Received on Thu Jan 15 2015 - 05:30:02 PST
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