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

From: Suri Moonsamy <suri_moonsamy.ymail.com>
Date: Tue, 23 Jul 2013 03:17:36 -0700 (PDT)

Hi Amber expert,

I need to run simulations for a protein, where some amino acids are phosphorylated and I came across the Contributed parameters 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.

Your assistance will be highly appreciated.

Kind regards,
Suri Moonsamy
Molecular Modeling and Drug Design
Discipline of Pharmaceutical Sciences
School of Health Science

Westville Campus
Private Bag X54001
Durban 4000
South Africa
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Received on Tue Jul 23 2013 - 03:30:02 PDT
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