[AMBER] Fwd: file contains 2 atoms not in residue templates

From: Vishal Nemaysh <vishal.bioinfotech.gmail.com>
Date: Tue, 23 Sep 2014 18:54:57 +0530

Sorry for forgetting the attachment of pdb file here the file is attached
---------- Forwarded message ----------
From: Vishal Nemaysh <vishal.bioinfotech.gmail.com>
Date: Tue, Sep 23, 2014 at 6:52 PM
Subject: file contains 2 atoms not in residue templates
To: AMBER Mailing List <amber.ambermd.org>




*Dear all, I am getting a error in leap while loading my .pdb file. How to
resolve it? the pdb file is also attached herewith. Thanks in advance*




Created a new atom named: OT1 within residue: .R<CGLU 102>
Created a new atom named: OT2 within residue: .R<CGLU 102>
  Added missing heavy atom: .R<CGLU 102>.A<O 15>
  Added missing heavy atom: .R<CGLU 102>.A<OXT 16>
  total atoms in file: 838
  Leap added 850 missing atoms according to residue templates:
       8 Heavy
       842 H / lone pairs
  The file contained 6 atoms not in residue templates
> check 1YCC
Checking '1YCC'....
WARNING: The unperturbed charge of the unit: 7.000000 is not zero.
FATAL: Atom .R<ILE 35>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 53>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 74>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 94>.A<CD 20> does not have a type.
FATAL: Atom .R<CGLU 102>.A<OT1 17> does not have a type.
FATAL: Atom .R<CGLU 102>.A<OT2 18> does not have a type.
Warning: Close contact of 1.420035 angstroms between .R<CALA -1>.A<OXT 11>
and .R<NGLY 1>.A<CA 5>
Warning: Close contact of 1.201258 angstroms between .R<CALA -1>.A<OXT 11>
and .R<NGLY 1>.A<H3 4>
Warning: Close contact of 0.800222 angstroms between .R<CALA -1>.A<OXT 11>
and .R<NGLY 1>.A<H2 3>
Warning: Close contact of 1.101083 angstroms between .R<CALA -1>.A<OXT 11>
and .R<NGLY 1>.A<H1 2>
Warning: Close contact of 0.239175 angstroms between .R<CALA -1>.A<OXT 11>
and .R<NGLY 1>.A<N 1>
Warning: Close contact of 1.054825 angstroms between .R<CALA -1>.A<C 9> and
.R<NGLY 1>.A<H2 3>
Warning: Close contact of 1.180566 angstroms between .R<CALA -1>.A<C 9> and
.R<NGLY 1>.A<H1 2>
Warning: Close contact of 1.345228 angstroms between .R<CALA -1>.A<C 9> and
.R<NGLY 1>.A<N 1>
Warning: Close contact of 1.404862 angstroms between .R<HIE 18>.A<HE2 13>
and .R<TYR 67>.A<HH 15>
Warning: Close contact of 0.916058 angstroms between .R<ILE 35>.A<HD13 17>
and .R<ILE 35>.A<CD 20>
Warning: Close contact of 1.200856 angstroms between .R<ILE 35>.A<HD12 16>
and .R<ILE 35>.A<CD 20>
Warning: Close contact of 0.733063 angstroms between .R<ILE 35>.A<CD1 14>
and .R<ILE 35>.A<CD 20>
Warning: Close contact of 0.983832 angstroms between .R<ILE 53>.A<HD13 17>
and .R<ILE 53>.A<CD 20>
Warning: Close contact of 1.028195 angstroms between .R<ILE 53>.A<HD12 16>
and .R<ILE 53>.A<CD 20>
Warning: Close contact of 1.323031 angstroms between .R<ILE 53>.A<HD11 15>
and .R<ILE 53>.A<CD 20>
Warning: Close contact of 0.241268 angstroms between .R<ILE 53>.A<CD1 14>
and .R<ILE 53>.A<CD 20>
Warning: Close contact of 0.966134 angstroms between .R<CPRO 71>.A<OXT 15>
and .R<NLYS 72>.A<H3 4>
Warning: Close contact of 0.934786 angstroms between .R<CPRO 71>.A<OXT 15>
and .R<NLYS 72>.A<H2 3>
Warning: Close contact of 1.038652 angstroms between .R<CPRO 71>.A<OXT 15>
and .R<NLYS 72>.A<H1 2>
Warning: Close contact of 0.187098 angstroms between .R<CPRO 71>.A<OXT 15>
and .R<NLYS 72>.A<N 1>
Warning: Close contact of 1.302412 angstroms between .R<CPRO 71>.A<O 14>
and .R<NLYS 72>.A<H2 3>
Warning: Close contact of 0.657667 angstroms between .R<CPRO 71>.A<C 13>
and .R<NLYS 72>.A<H2 3>
Warning: Close contact of 1.344875 angstroms between .R<CPRO 71>.A<C 13>
and .R<NLYS 72>.A<N 1>
Warning: Close contact of 1.229195 angstroms between .R<ILE 74>.A<HD13 17>
and .R<ILE 74>.A<CD 20>
Warning: Close contact of 0.937205 angstroms between .R<ILE 74>.A<HD12 16>
and .R<ILE 74>.A<CD 20>
Warning: Close contact of 1.135349 angstroms between .R<ILE 74>.A<HD11 15>
and .R<ILE 74>.A<CD 20>
Warning: Close contact of 0.180495 angstroms between .R<ILE 74>.A<CD1 14>
and .R<ILE 74>.A<CD 20>
Warning: Close contact of 0.968481 angstroms between .R<ILE 94>.A<HD13 17>
and .R<ILE 94>.A<CD 20>
Warning: Close contact of 1.018878 angstroms between .R<ILE 94>.A<HD12 16>
and .R<ILE 94>.A<CD 20>
Warning: Close contact of 1.396182 angstroms between .R<ILE 94>.A<HD11 15>
and .R<ILE 94>.A<CD 20>
Warning: Close contact of 0.314511 angstroms between .R<ILE 94>.A<CD1 14>
and .R<ILE 94>.A<CD 20>
Warning: Close contact of 0.828062 angstroms between .R<CGLU 102>.A<OXT 16>
and .R<CGLU 102>.A<OT2 18>
Warning: Close contact of 0.577675 angstroms between .R<CGLU 102>.A<O 15>
and .R<CGLU 102>.A<OT1 17>
Warning: Close contact of 1.260318 angstroms between .R<CGLU 102>.A<C 14>
and .R<CGLU 102>.A<OT1 17>
Warning: Close contact of 1.259888 angstroms between .R<CGLU 102>.A<C 14>
and .R<CGLU 102>.A<OT2 18>
Checking parameters for unit '1YCC'.
Checking for bond parameters.
Checking for angle parameters.
check: Errors: 6 Warnings: 36
-- 
Vishal
Research Scholar,
Neuropharmaceutical Chemistry lab.,
Dr. B. R. Ambedkar Center for Biomedical Research,
University of Delhi, Delhi-110007
Email: *vishal.bioinfotech.gmail.com <vishal.bioinfotech.gmail.com>*
Phone: 91-11-27662778 Mobile: 91+9650736653
-- 
Vishal
Research Scholar,
Neuropharmaceutical Chemistry lab.,
Dr. B. R. Ambedkar Center for Biomedical Research,
University of Delhi, Delhi-110007
Email: *vishal.bioinfotech.gmail.com <vishal.bioinfotech.gmail.com>*
Phone: 91-11-27662778 Mobile: 91+9650736653



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Received on Tue Sep 23 2014 - 06:30:03 PDT
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