AMBER Archive (2009)

Subject: Re: [AMBER] non standart residue library creation with tleap (Zn atom)

From: Andrew Voronkov (drugdesign_at_yandex.ru)
Date: Fri Nov 20 2009 - 09:07:26 CST

Ok, thank you. This helps moving forward.
I have built Zn library in the attachment for the pdb file (in attachment, PDB code is 2rf5), but I still get the error message even after loadoff zna.lib

> tnk = loadpdb 2rf5-znparm.pdb
Loading PDB file: ./2rf5-znparm.pdb
Unknown residue: ZN number: 207 type: Terminal/last
.relaxing end constraints to try for a dbase match
  -no luck
  Added missing heavy atom: .R<MET 1207>.A<CG 8>
  Added missing heavy atom: .R<MET 1207>.A<SD 11>
  Added missing heavy atom: .R<MET 1207>.A<CE 12>
  Added missing heavy atom: .R<PHE 1208>.A<CG 8>
  Added missing heavy atom: .R<PHE 1208>.A<CD1 9>
  Added missing heavy atom: .R<PHE 1208>.A<CD2 17>
  Added missing heavy atom: .R<PHE 1208>.A<CE1 11>
  Added missing heavy atom: .R<PHE 1208>.A<CE2 15>
  Added missing heavy atom: .R<PHE 1208>.A<CZ 13>
  Added missing heavy atom: .R<THR 1265>.A<CG2 7>
  Added missing heavy atom: .R<THR 1265>.A<OG1 11>
  Added missing heavy atom: .R<CGLU 1310>.A<OXT 16>
Creating new UNIT for residue: ZN sequence: 1311
Created a new atom named: ZNA within residue: .R<ZN 1311>
  total atoms in file: 1665
  Leap added 1628 missing atoms according to residue templates:
       12 Heavy
       1616 H / lone pairs
  The file contained 1 atoms not in residue templates

Best regards,
Andrew

20.11.09, 08:30, "case" <case_at_biomaps.rutgers.edu>:

> On Fri, Nov 20, 2009, Andrew Voronkov wrote:
> >
> > I've saved Zn into a separate PDB file as in this tutorial:
> > http://www.rosswalker.co.uk/tutorials/amber_workshop/Tutorial_four/section2.htm
> >
> > Here are PDB file contents:
> > HETATM 1666 ZNA ZN A 1 -34.053 -24.945 -27.759 1.00 27.33 ZN
> > END
> >
> > Then I've loaded it as zna = loadpdb zna.pdb and tried to set the atom
> > type and charge according the command which yo have provided in
> > format set unit.resnumber.resname type Zn. But I've got an error about that this is "not a containter".
> >
> >
> > > desc zna
>
> Use more detailed "desc" commands (as suggested earlier):
> desc zna.1 will show atoms in the residue
> desc zna.1.ZNA will describe the atom; I'm guessing from your PDB file
> that the atom name is "ZNA", not "ZN", but the desc
> command will let you know for sure.
>
> ...dac
>
>
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>

  • application/octet-stream attachment: zna.lib


  • application/octet-stream attachment: zna.pdb

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