AMBER Archive (2009)

Subject: [AMBER] Phosphothreonine

From: Beale, John (John.Beale_at_stlcop.edu)
Date: Thu Nov 05 2009 - 07:03:58 CST

I am trying to use leap to create the files for a protein with a
threonine residue that is phosphorylated at the side chain hydroxyl
group. I went to the site http://pharmacy.man.ac.uk/amber/ and
downloaded the *.off and frcmod files for phosphothreonine. When I set
up leap I did the following:

 

xleap -s -f leaprc.ff99SB

loadOff T2P.off

loadAmberParams frcmod_t2p

test = loadPdb myfile.pdb

 

Leap gave me some complaints:

 

Created a new atom named: P1 within residue: .R <THR 315>

Created a new atom named: O3 within residue: .R <THR 315>

Created a new atom named: O2 within residue: .R <THR 315>

Created a new atom named: O1 within residue: .R <THR 315>

Created a new atom named: H1 within residue: .R <THR 315>

 

Added missing heavy atom .R< CMET 416> .A<OXT 18>

Leap added 5 missing atoms not in residue templates:

 

1 heavy

4H/lone pairs

 

The file contained 5 atoms not in residue templates. Since added/missing
= extra, there is a high probability

of atoms with 'incorrect' names; you may want to use addPdbAtomMap to
map these names, or change in file.

 

When I do "saveAmberParm" test *.prmtop *.inpcrd, I get the following:

 

FATAL: Atom .R<THR 315>.A<P1 15> does not have a type.

FATAL: Atom .R<THR 315>.A<O3 16> does not have a type.

FATAL: Atom .R<THR 315>.A<O2 17> does not have a type.

FATAL: Atom .R<THR 315>.A<O1 18> does not have a type.

FATAL: Atom .R<THR 315>.A<H1 19> does not have a type.

 

Failed to generate parameters

Parameter file was not saved.

 

What do I need to do to correct this so that I can generate parameters
for the phosphorylated protein?

 

Thanks!

 

John

 

 

 

 

 

 

 

 

 

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