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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Received on Thu Nov 05 2009 - 05:30:03 PST
