Re: [AMBER] Simulation of the docked complex with phosphorylated tyrosine

From: David A Case <>
Date: Thu, 3 Dec 2015 08:33:30 -0500

On Thu, Dec 03, 2015, Pallavi Mohanty wrote:

> I have a docked complex with one the tyrosines is phosphorylated. The
> phosphorylated tyrosine is interacting with some residues present in the
> other chain of the complex. I have performed the docking in HADDOCK. Now I
> want to simulate the complex and I am clueless what can be the possible
> strategy. As in i am unable to generate the topology and coordinate files
> for the complex. Moreover I thought antechamber would be the possible
> answer but unfortunately it says MAXATOM limit exceeds the given input.

Amber provides standard libraries for common phosphorylated amino acids: use
the leaprc.phosaa10 file as well as leaprc.ff14SB. See Section 3.2 of the
2015 Amber Reference Manual. Note: because the PDB standard does not
distinguish between protonated and deprotonated phosphates, some Amber residue
names are non-standard, and you will have to edit your PDB file so that the
Amber library names are used. See the comments at the top of the
leaprc.phosaa10 file.

Based on very limited information, the error in antechamber may have arisen
because you gave it an entire protein or complex file. Antechamber is
intended for *single residues or small molecules* only.

...good luck...dac

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Received on Thu Dec 03 2015 - 06:00:03 PST
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