AMBER Archive (2009)

Subject: Re: [AMBER] Phosphothreonine

From: Anselm Horn (Anselm.Horn_at_biochem.uni-erlangen.de)
Date: Thu Nov 05 2009 - 07:17:59 CST

Dear John,

please ensure that the atom names of the T2P residue in your pdb file
are consistent with those of the parameter file, i.e. rename
P1 -> P, O1 -> O1P, O2 -> O2P, O3 -> O3P etc

Have a look at the structure of T2P with xleap if in doubt about the
correct names.

Regards,

Anselm

Bioinformatik
Emil-Fischer-Zentrum
Friedrich-Alexander-Universität Erlangen-Nürnberg
Erlangen
Germany

Beale, John wrote:
> 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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>
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>

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