[AMBER] Issue with preparing pdb, top and crd files via leap for a non-standard residue

From: Valerie Fako <vfako.iupui.edu>
Date: Wed, 21 Jul 2010 17:29:54 -0400

Hello Everyone,

I am trying to prepare the solvated pdb, top, and crd files to run an MD
simulation for a protein/ligand complex. I have a non-standard residue in
my protein: a serine residue that has a ligand covalently bonded to it. I
followed the AMBER Advanced Tutorial A1: Setting Up and Advanced System to
prepare my serine-ligand/protein complex. I defined the backbone N and
backbone C of the serine residue/ligand complex that will be connected to
the protein via xleap, as mentioned in AMBER Tutorial 4: Simulating a
Solvated Protein that Contains Non-Standard Residues. Prior to running
xleap or tleap, the protein bonds between the serine/ligand residue and the
adjacent residues are recognized both by xleap (as examined with the
graphical interface) and Chimera.

The issue arrises when I try to write the solvated pdb, top and crd files
using xleap or tleap. The files are written, but when I look at the
solvated pdb via Chimera, only the backbone N bond from the serine to
the adjacent residue is recognized, the other bond, from the backbone C of
the serine to the other adjacent residue is no longer recognized, and a TER
has been placed in the pdb between the serine/ligand residue and the
adjacent residue (there is no TER placed in the pdb at the on the other side
of the residue). Any ideas of why this might be happening and how I might
go about fixing my files so that no TER is written into the solvated pdb and
both protein bonds are recognized? Is there any way to get around this?

Any help or insight would be greatly appreciated!

Thank you,

Valerie Fako
Department of Pharmacology
Indiana University School of Medicine
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Received on Wed Jul 21 2010 - 15:00:03 PDT
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