On Mon, Jul 23, 2012 at 3:51 AM, kamlesh sahu <kamleshsemail.gmail.com>wrote:
> Hello,
>
> I have simulated a a dimer (protein A and B) in complex with two ligands C
> and D. While making prmtop and inpcrd files, protein A and B together was
> treated as receptor and C abd D were treated as ligands (see below for the
> input file plz). Now I wish to calculate the binding energy of A and B.
>
I don't see an input file.
> 1- Can I use the same trajectories where I provide protein A as receptor in
> receptor_mask and protein B as ligand ? Will this require creation of new
> prmtop files where I feed A as receptor and B as ligand to tleap ?
>
Yes you can use the same trajectories (so long as you understand the
approximation that you're making -- namely that the conformational states
sampled by a subset of your system is the same as in both the bound and
free states). Yes, you will need a complex prmtop that has the residues of
both A and B, a receptor prmtop that is just residues A, and a ligand
prmtop that is just residues B.
2- Do I need to strip C and D from the trajectories by adding residue names
> in strip_mask list ?
>
If they are not in either the receptor or ligand, yes you do.
>
> Thank you
> Regards,
> kamlesh
>
I'm confused. Do you still have an error? Just horribly wrong binding
free energies? Is everything working, just the C/D, or is nothing working?
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Jul 23 2012 - 05:00:03 PDT
