[gmx-users] free energy calculation on amino acid mutation

[Mark Abraham]

Hi,

I understand pmx is built exactly for this task.

Mark

On Thu, 26 May 2016 19:35 <hannes.loeffler at stfc.ac.uk> wrote:

> That really depends on how you approach the problem.
>
> When you choose a dual topology approach you would need to decide where to
> branch off but basically end up with duplicating parts of the residue.
> Sounds like that's what you were trying to do.
>
> In the single topology approach you would match as many atoms as possible
> and balance just the missing atoms with dummies (as opposed to the dual
> approach where you may have lots of them).  As the bonded network stays the
> same you would not need to make any modifications to those.  I do not see
> any reason why you would not want to use this approach in your specific
> case (LEU->GLY).
>
> There is a tool out there that you should probably give a try: pmx.  I
> believe it uses the single topology approach.
>
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of Yi An [
> anyiphysics at gmail.com]
> Sent: 26 May 2016 17:44
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] free energy calculation on amino acid mutation
>
> Hi Gromacs users,
>
> I'm trying to calculate the relative binding free energy of a certain
> ligand when a leucine in the ligand binding site is mutated to glycine. The
> concept is simple but I have met some difficulties creating topology files
> for free energy calculation. I have two questions I wish you guys can help:
>
> 1. Let's say my protein have 200 residues and the leucine I want to mutate
> is in the middle (80 for example). When I tried to edit the topology of
> this protein, I found that since the number of atoms changed, I need to
> make lots of changes for bond, angle, and dihedral parameters. Is my
> feeling correct?
>
> 2. If my understanding is correct, I wish there are some existing scripts
> which can help people create topology file for mutational free energy
> calculation. I will highly appreciate if you guys tell me where I can find
> them.
>
> Thank you very much.
>
>
> Yi An
> Postdoctoral Research Associate
> UNC-Chapel Hill
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