AMBER Archive (2009)

Subject: [AMBER] RE: Amber question

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Thu Dec 24 2009 - 17:44:54 CST

Hi Gunaydin,

I am cc'ing this to the AMBER mailing list which is the best place for such
questions.

The limitation you are referring to here is the use of Belly constraints for
GB simulations. It does not affect explicit solvent calculations.
Unfortunately what you suggest will not work since Leap depends on the chain
being in the correct order to get the connectivity.

You could force it if your region to fix is continuous. Move this to the top
- as complete residues and then add a TER card at the end. Then load it into
leap and manually bind the two ends together with the bond command. This may
take some tweaking to get to work due to issues with Leap adjusting the
terminal residues of a chain.

A better option would be to use harmonic restraints (ntr=1) in place of
belly constraints. These do not have the limitation on only restraining the
beginning of the prmtop.

All the best
Ross

> -----Original Message-----
> From: gunaydin_at_chem.ucla.edu [mailto:gunaydin_at_chem.ucla.edu]
> Sent: Monday, December 21, 2009 12:22 PM
> To: ross_at_rosswalker.co.uk
> Subject: Amber question
>
> Dear Ross,
>
> I have a rather beginner's question. I want to run a MD simulation with
> implicit solvent model. In addition, I want to fix some of the
> residues.
> As far as I understand, moving residues need to be at the top of the
> pdb
> file. So, let's assume that I have a protein with three residues {ALA,
> GLY, VAL}.
>
> I want to let GLY move during the MD run but keep ALA and VAL fixed.
> So, I
> need to rearrange my pdb file so that it is {GLY, ALA, VAL}. Is this
> correct?
>
> If so, this present a problem because leap connects the carbonyl group
> of
> GLY to the amine group of ALA. However, in the real life, the carbonyl
> group of ALA needed to be connected to the amine group of the GLY.
>
> I assume there is an easy fix for this problem. How am I supposed to
> keep
> the sequence as GLY, ALA and VAL and have ALA show up at the top of the
> PDB file for amber calculation?
>
> Thanks,
> -Hakan

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