hi dear. thanks for your answer.
but yes i downloaded it from pdb.org. i was wondering if it would be
feasible to process the pdb file with red-tools?
El 16/10/2012 05:14, "Carlos Simmerling" <carlos.simmerling.gmail.com>
escribió:
> 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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> >
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Received on Tue Oct 16 2012 - 07:30:04 PDT
