Hello Rima,
I'm not an expert but I could share some of my experience with you.
>> To generate the snapshots, does the mdcrd files have to be stripped off
water and counterions?
yes
>>whereas the prmtop files for the lig/receptor/complex being the unsolvated
prmtops??
yes, you need to generate prmtop for each of the system: lig, receptor and
complex, without any water/ions.
>>Also, in the extract_coord.in it mentions that the NTOTAL flag must list
the total number of atoms including water and ions, so that again confuses
me, as in what should the coordinate file be??
as explained in the amber manual, NTOTAL is the total number of atoms in
your MD trajectory (inclusive wat and ions). The first step of calculating
binding free energy using MMPBSA needs trajectory of each system: lig, com
and rec. The make_crd_hg will extract these for you from your existing MD
trajectory.
The idea behind MMPBSA is to run an explicit MD first before using continuum
representation of polar (PB) and non-polar (SA) contribution to give you
estimation of the binding free energy. Probably you can get more information
about this methodology from literatures.
Good luck!
Regards,
Vanessa
On 2/7/07, Rima Chaudhuri <rima.chaudhuri.gmail.com> wrote:
>
> Dear Amberites,
>
> I am a novice at MM-PBSA, trying to calculate the binding free energy of
> my protein-ligand system. However, I have certain outstanding questions
> after having read through the literature and going through some of the
> archive messages here:
> 1) To generate the snapshots, does the mdcrd files have to be stripped off
> water and counterions? or should this be the mdcrd out of the MD-run (with
> explicit water) ? whereas the prmtop files for the lig/receptor/complex
> being the unsolvated prmtops?? I could not find anything conclusive from the
> archive and am left undecided.My guess is, it should be stripped? but in
> the amber tutorial, I did not find any mention of it. Also, in the
> extract_coord.in it mentions that the NTOTAL flag must list the total number
> of atoms including water and ions, so that again confuses me, as in what
> should the coordinate file be??
>
> 2) I tried using the snapshots generated from the mdcrd file with explicit
> water, for the MM-PBSA-binding calculation and land up getting the error of
> 'No values for MM ELE existing >> ' which made me think that the snapshots
> may need to be generated off the stripped co-ordinate file....please
> confirm.
>
> Again, if the snapshots generated in the beginning are not from the
> explicit water coordinate file, and so the following binding energy
> calculations, what is the purpose of running the simulation with explicit
> water/periodic boundary conditions for MM-PBSA purposes? Maybe I
>
> thanks a lot in advance...
> -Rima
>
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Received on Wed Feb 14 2007 - 06:07:36 PST
