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

From: Levi Pierce <>
Date: Wed, 21 Jul 2010 14:40:11 -0700


  My first suggestion is to just try to build your protein w/o solvating
it. I
have done this for numerous non-standard residues now and through a
combination of Ross Walker's great tutorials and my own hacking I have
a simple protocol to build non-standard residues. I don't like xleap I much
prefer putting all my commands in a leaprc file and simply running tleap. I
examine the resulting prmtop and crd file in vmd. Try to write these files
out just for the protein I don't think solvation should have anything to do
with your problem. I can send you an example leaprc file if you are


On Wed, Jul 21, 2010 at 2:29 PM, Valerie Fako <> wrote:

> 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
> _______________________________________________
> AMBER mailing list

Levi C.T. Pierce,  UCSD Graduate Student
McCammon Laboratory <>
w: 858-534-2916
AMBER mailing list
Received on Wed Jul 21 2010 - 15:00:04 PDT
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