Re: [AMBER] Amber for phophorylated residue

From: Ziba Bahadori <>
Date: Thu, 23 Jul 2015 15:27:39 +0000 (UTC)

thanks for your guidance

     On Thursday, July 23, 2015 7:15 PM, David A Case <> wrote:

 On Thu, Jul 23, 2015, Ziba Bahadori wrote:

> I want to do MD simulation of a phosphorylated
> protein. Will you please tell me from the
> unphosphorylated protein, how can we get the
> coordinate file of the phosphorylated protein?

Depends on how big the conformational change is upon phosphorylation.  You can
have LEaP just build the phosphate groups in a simple fashion onto the
unphosphorylated side chains, and hope that minimization and MD will lead to a
reasonable structure.  But larger conformational changes will probably not be
achieved by this, and you will need to use other tools (homology modeling
programs, Rosetta, etc.).  Amber does not have tools to predict protein
structures from sequence.

> then how can we get the parmtop and inpcrd files?

You should source leaprc.phosaa10 to load the libraries for phosphorylated
amino acids.  You should check that the atom and residue names in your PDB
file match those in the libraries.  (We try to follow PDB nomenclature, but
the protein data bank doesn't distinguish between the -1 and -2 protonation

...good luck...dac

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