it sounds like a problem with the PDB file- you should look at it and check
to see if the warnings are correct. Where did you get the pdb file? if not
from the pdb, check with the person or program that generated it.
On Tue, Oct 16, 2012 at 1:16 AM, Carlos Romero <carlos.rom.74he.gmail.com>wrote:
> 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 Tue Oct 16 2012 - 03:30:02 PDT
