Hi dear Amber user's
When I use tleap in order to load my protein, there are warnings that say:
Warning: name change in pdb file residue 1 ;
this residue is split into SER and GLU.
Warning: name change in pdb file residue 1 ;
this residue is split into GLU and TYR.
Warning: name change in pdb file residue 1 ;
this residue is split into TYR and GLN.
Warning: name change in pdb file residue 1 ;
this residue is split into GLN and THR.
Warning: name change in pdb file residue 1 ;
this residue is split into THR and PHE.
......ETC,
96 residues had naming Warnings.
There are split Residues;
residue sequence number will not correspond to those in the pdb.
-- residue 6: duplicate [ C] atoms (total 2)
-- residue 6: duplicate [ CA] atoms (total 2)
-- residue 6: duplicate [ CB] atoms (total 2)
-- residue 6: duplicate [ CD1] atoms (total 2)
-- residue 6: duplicate [ CD2] atoms (total 2)
-- residue 6: duplicate [ CE1] atoms (total 2)
-- residue 6: duplicate [ CE2] atoms (total 2)
-- residue 6: duplicate [ CG] atoms (total 2)
-- residue 6: duplicate [ CZ] atoms (total 2)
-- residue 6: duplicate [ N] atoms (total 2)
-- residue 6: duplicate [ O] atoms (total 2)
-- residue 37: duplicate [ C] atoms (total 2)
-- residue 37: duplicate [ CA] atoms (total 2)
-- residue 37: duplicate [ CB] atoms (total 2)
-- residue 37: duplicate [ CD1] atoms (total 2)
-- residue 37: duplicate [ CD2] atoms (total 2)
-- residue 37: duplicate [ CE1] atoms (total 2)
-- residue 37: duplicate [ CE2] atoms (total 2)
-- residue 37: duplicate [ CG] atoms (total 2)
-- residue 37: duplicate [ CZ] atoms (total 2)
-- residue 37: duplicate [ N] atoms (total 2)
-- residue 37: duplicate [ O] atoms (total 2)
...........ETC
Warning: Atom names in each residue should be unique.
(Same-name atoms are handled by using the first
ocurrence and by ignoring the rest.
Frequently duplicate atom names stem form alternate
conformations in the PDB file.)
Added missing heavy atom: .R<NSER 1> .A<OG 10>
Added missing heavy atom: .R<GLU 2> .A<CG 8>
Added missing heavy atom: .R<GLU 2> .A<CD 11>
Added missing heavy atom: .R<GLU 2> .A<OE1 12>
Added missing heavy atom: .R<GLU 2> .A<OE2 13>
Added missing heavy atom: .R<CASP 42> .A<OXT 13>
Added missing heavy atom: .R<CPHE 291> .A<OXT 21>
Added missing heavy atom: .R<CGLU 300> .A<OXT 16>
......ETC
total atoms in file 4929
leap added 4806 missing atoms according to residue templates:
11 heavy
4795 H / lone pairs
>
After that I saved prmtop and inpcrd files, then with ambpdb I saved my
file.pdb but when I checked my pdb file every residue is in disorder
if anyone could help me please I will appreciate a lot
I have installed Ubuntu 10.10, AmberTools 1.4 Amber11
thanks in advance
Regards
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Received on Mon Oct 15 2012 - 22:30:03 PDT
