Re: [AMBER] setting up non-standard amino acid residues for MD simulation

From: David A. Case <>
Date: Tue, 23 Jul 2013 10:04:26 -0400

On Tue, Jul 23, 2013, Suri Moonsamy wrote:
> I need to run simulations for a protein, where some amino acids are
> phosphorylated and I came across theĀ Contributed parametersĀ database,
> where there are files for for Tyrosine and Theroerine with phosphate
> groups. I need assistance with the technical steps that I should follow,
> starting from editing the PDB structures to create phoshorylated PDB
> amino acid structures and up until to run the simulations.

AmberTools13 has these residues "built-in". See
$AMBERHOME/dat/lib/lib/phosaa10.readme. Basically, you load the "phosaa"
files, and proceed as with a normal protein. You may need to pay more that
usual attention to making sure that the atom and residue names in your PDB
file match those in the library. Also, as with histidine, you need to decide
which protonation state you want.

...good luck....dac

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Received on Tue Jul 23 2013 - 07:30:02 PDT
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