Hello Anselm
Thanks for your reply.
I did the same as u said. I also changed the name of TPO as T2P in the PDB,
but the error persists as shown below:
v = loadpdb protein.pdb
Loading PDB file: ./protein.pdb
Unknown residue: T2P number: 162 type: Terminal/beginning
..relaxing end constraints to try for a dbase match
-no luck
Added missing heavy atom: .R<CTYR 177>.A<OXT 22>
Creating new UNIT for residue: T2P sequence: 178
Created a new atom named: N within residue: .R<T2P 178>
Created a new atom named: CA within residue: .R<T2P 178>
Created a new atom named: C within residue: .R<T2P 178>
Created a new atom named: O within residue: .R<T2P 178>
Created a new atom named: CB within residue: .R<T2P 178>
Created a new atom named: CG2 within residue: .R<T2P 178>
Created a new atom named: OG1 within residue: .R<T2P 178>
Created a new atom named: P within residue: .R<T2P 178>
Created a new atom named: O1P within residue: .R<T2P 178>
Created a new atom named: O2P within residue: .R<T2P 178>
Created a new atom named: O3P within residue: .R<T2P 178>
One sided connection. Residue: missing connect1 atom.
total atoms in file: 2417
Leap added 2418 missing atoms according to residue templates:
1 Heavy
2417 H / lone pairs
The file contained 11 atoms not in residue templates
Please help me out with suitable suggestion.
Regards.
On Mon, Jun 6, 2011 at 2:45 AM, Anselm Horn <
Anselm.Horn.biochem.uni-erlangen.de> wrote:
> Hi Nitu,
>
> > They
> > also provided the web
> > link ( http://pharmacy.man.ac.uk/amber/) for downloading these
> parameters.
>
> right, the parameters of the phosphorylated amino acids Thr, Tyr, Ser,
> and His are provided there.
>
> > Unfortunately those are not loading although we have tried it by changing
> > the residue name of TPO by T1P in our pdb, still the error is same
> > Please send me the parameters file for TPO,
>
> It is difficult to analyse what was going wrong without your explicit
> commands and the resulting errors, and "those are not loading" is not
> very helpful here.
>
> Firstly, make sure that you correctly downloaded the parameter files and
> stored them in a directory accessible to leap; you could simply use the
> same directory as your other input files.
> Then load the provided library files during your preparation step within
> leap. Ensure, that your phosphothreonine residue in your input file (pdb
> ?) is named according to the parameter file residue (T1P, T2P ...), and
> that the names of the atoms in your input file (pdb) do match the names
> of those in the parameter file, this is crucial.
>
> Regards,
>
> Anselm
>
> Bioinformatik
> Inst. f. Biochemie
> Friedrich-Alexander-Universität Erlangen-Nürnberg
> Germany
>
>
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Nitu Bansal
M.S Pharm
Research Scholar
Department of Pharmacoinformatics
S.A.S Nagar NIPER Mohali (Chandigarh)
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Received on Mon Jun 06 2011 - 10:30:07 PDT
