Hi DAC!
I executed a previous minimization of energies but now
when i load a new model which contains a protein binding to DNA tleap adds
3 atoms, after run >check COMPLEX command, the result indicates me that
these atoms do not have a type, i already read the pdb file using text edit
but the atom coordinates are ok, how i can solve these problem,
these are the atoms added by tleap
ATOM 1615 P DC C 192 -10.353 839.368 -0.187 1.00145.06
P
ATOM 1616 OP1 DC C 192 -10.318 838.517 -1.406 1.00145.06
O
ATOM 1617 OP2 DC C 192 -11.450 839.206 0.790 1.00145.06
O
these are my commands:
N-terminal-2:VACUM javieralejandrorendoncarrillo$ tleap -s -f
$AMBERHOME/dat/leap/cmd/leaprc.ff99SB
> COMPLEX = loadpdb complex.pdb
Loading PDB file: ./complex.pdb
(starting new molecule for chain B)
(starting new molecule for chain C)
Added missing heavy atom: .R<DA5 181>.A<O5' 2>
Created a new atom named: P within residue: .R<DC5 192>
Created a new atom named: OP1 within residue: .R<DC5 192>
Created a new atom named: OP2 within residue: .R<DC5 192>
Added missing heavy atom: .R<DA3 202>.A<C5' 5>
Added missing heavy atom: .R<DA3 202>.A<C4' 8>
Added missing heavy atom: .R<DA3 202>.A<O4' 10>
Added missing heavy atom: .R<DA3 202>.A<C3' 27>
Added missing heavy atom: .R<DA3 202>.A<C1' 11>
Added missing heavy atom: .R<DA3 202>.A<C2' 29>
Added missing heavy atom: .R<DA3 202>.A<O3' 32>
Added missing heavy atom: .R<DA3 202>.A<N9 13>
Added missing heavy atom: .R<DA3 202>.A<C8 14>
Added missing heavy atom: .R<DA3 202>.A<C4 26>
Added missing heavy atom: .R<DA3 202>.A<N7 16>
Added missing heavy atom: .R<DA3 202>.A<C5 17>
Added missing heavy atom: .R<DA3 202>.A<N3 25>
Added missing heavy atom: .R<DA3 202>.A<C6 18>
Added missing heavy atom: .R<DA3 202>.A<C2 23>
Added missing heavy atom: .R<DA3 202>.A<N6 19>
Added missing heavy atom: .R<DA3 202>.A<N1 22>
total atoms in file: 1821
Leap added 1708 missing atoms according to residue templates:
18 Heavy
1690 H / lone pairs
The file contained 3 atoms not in residue templates
> check COMPLEX
Checking 'COMPLEX'....
WARNING: The unperturbed charge of the unit: -9.000000 is not zero.
*FATAL: Atom .R<DC5 192>.A<P 29> does not have a type.*
*FATAL: Atom .R<DC5 192>.A<OP1 30> does not have a type.*
*FATAL: Atom .R<DC5 192>.A<OP2 31> does not have a type.*
*-- *
LBG Javier Alejandro Rendón Carrillo
Laboratorio de Investigación y Desarrollo
Tel. (044) 81-80-52-05-76
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Received on Tue May 07 2013 - 01:00:03 PDT
