Re: [AMBER] prep files ATP-MG++ and for phosphorylated threonine

From: Anselm Horn <>
Date: Sun, 05 Jun 2011 23:15:04 +0200

Hi Nitu,

> They
> also provided the web
> link ( 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.



Inst. f. Biochemie
Friedrich-Alexander-Universität Erlangen-Nürnberg

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Received on Sun Jun 05 2011 - 14:30:03 PDT
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