AMBER Archive (2007)

Subject: AMBER: help with phosphotyrosine

From: Samantha Kaye (samantha.kaye_at_pharmacy.ac.uk)
Date: Mon Jul 16 2007 - 10:45:36 CDT

I realise this question has been asked before but I can't find a definitive
answer, how do I parameterise a phosphotyrosine residue?

The background to my problem is as follows. This is my first project using
Amber but I have successfully set up a simulation of the unphosph version of
my protein. In order to set up a phosph version I added the phosphate group
in insightII then hand edited the PDB file so that the group was connected
and part of the same residue. I then renumbered the atoms in the file. The
pTyr residues is currently labelled as a TYR residue type (rather than PTR
as it would be in a PDB file).

I have tried to load the file into xleap (using ff99SB) and get this output:

model=loadpdb trunc_prot.pdb

Loading PDB file: ./trunc_prot.pdb

Created a new atom named: P1 within residue: .R<TYR 386> Created a new atom
named: O2 within residue: .R<TYR 386> Created a new atom named: O3 within
residue: .R<TYR 386> Created a new atom named: O4 within residue: .R<TYR
386> Created a new atom named: O5 within residue: .R<TYR 386>

Added missing heavy atom: .R<TYR 386>.A<OH 14>

 total atoms in file: 3210

 Leap added 3217 missing atoms according to residue templates:

 1 Heavy

 3216 H / lone pairs

 The file contained 5 atoms not in residue templates > saveamberparm

 model trunc_prot.prmtop trunc_prot.inpcrd Checking Unit.

 WARNING: The unperturbed charge of the unit: 1.000000 is not zero.

 FATAL: Atom .R<TYR 386>.A<P1 22> does not have a type.

 FATAL: Atom .R<TYR 386>.A<O2 23> does not have a type.

 FATAL: Atom .R<TYR 386>.A<O3 24> does not have a type.

 FATAL: Atom .R<TYR 386>.A<O4 25> does not have a type.

 FATAL: Atom .R<TYR 386>.A<O5 26> does not have a type.

 Failed to generate parameters

 Parameter file was not saved.

 

 Please can someone offer me some advice as I'm new to the program and don't
know where to start looking (perhaps antechamber?).

 Best wishes

 Samantha Kaye

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