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

From: Anselm Horn <>
Date: Tue, 07 Jun 2011 01:14:26 +0200

Hi Nitu,

> 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

obviously, leap does not recognize the T2P residue, maybe the parameters
were not read in correctly? What did you specify within your leap input?


1, Download the respective parameter files (e.g. T1P.lib, frcmod_t1p)
and store them into the directory where you invoke leap from.
2, Setup your tleap-input like:
# Protein with singly protonated phospho-threonine
source leaprc.ff99SB
loadoff T1P.lib
a=loadamberparams frcmod_t1p

protein=loadpdb "protein_inp.pdb"
saveamberparm protein prot.crd
savepdb protein prot.pdb
# End
3, Ensure that in your input pdb phospho-threonine has the residue name T1P.
4, Ensure that in your input pdb phospho-threonine's atoms have the
identical names as in the parameter files.
5, Run tleap and examine the output

Note, that the provided parameters do not work for terminal residues.



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

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Received on Mon Jun 06 2011 - 16:30:02 PDT
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