Peter,
if I understand you correctly, you wonder whether in a "stability"
calculation of a complex and a "binding energy" calculation for the same
complex with definition of receptor and ligand within the MMPBSA
framework the energies of the complex should be similar/same, if the
same parameters and structures are used.
The simple answer is, to the best of my knowledge, yes.
In a stability calculation, the energy of the complex system is
described in the same way as the energy contribution of the complex in a
binding calculation.
[Large discrepancies/differences in the energy may result from input
inconsistencies (e.g. different snapshots), mixed-up file naming (e.g.
wrong top files) or something similar.]
Maybe this helps.
Best,
Anselm
Bioinformatik | NHR.FAU
Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)
Germany
Am 29.01.2024 um 20:07 schrieb Ramdhan,Peter A via AMBER:
> I am trying to calculate the total energy of the complex. To describe the system, its a ligand-receptor complex which are both proteins. I performed some mutations on the ligand, ran a MD, then used mmpbsa to measure the binding free energy, and then compared it to that of the WT.
>
> Now, I just want to do the stability calculation of the complex itself.
>
> For commands in my receptor-ligand mutational studies, I used:
>
>
> $AMBERHOME/bin/MMPBSA.py -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -sp com.parm7 -cp com-dry.parm7 -rp rec.parm7 -lp lig.parm7 -y prod4.nc
>
>
> For the stability calculation, I used:
>
> $AMBERHOME/bin/MMPBSA.py -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -sp com.parm7 -cp com-dry.parm7 -y prod4.nc
>
> Sincerely,
>
> Peter Ramdhan, PharmD
> University of Florida College of Pharmacy
>
> [cid:b4858ce3-54d2-449b-8a23-19d8153c90ee]
> ________________________________
> From: Bill Miller III via AMBER <amber.ambermd.org>
> Sent: Wednesday, January 24, 2024 2:40 PM
> To: Ramdhan,Peter A via AMBER <amber.ambermd.org>
> Subject: Re: [AMBER] MMPBSA Stability Calculations
>
> [External Email]
>
> So you’re trying to calculate a binding free energy between a receptor and a ligand, or are you just trying to calculate the total energy of the complex?
>
> Also, what were the exact commands that you tried for each setup you stated?
>
> -Bill
>
>> On Jan 24, 2024, at 7:53 AM, Ramdhan,Peter A via AMBER <amber.ambermd.org> wrote:
>>
>> Hello,
>>
>> I am attempting to start stability calculations using mmpbsa. The manual states to only prompt the program to use the complex parm7 file, which I am prompting both solvated and de-solvated files. Upon completion, I receive a large positive G value (19690.8588).
>> I compared this to a mmpbsa calculation using the receptor and ligand with the exact same parameters (indi, etc.) and frames but I received a negative number for the complex instead which is -13587.4419. Should I expect similar outputs for the complex regardless of specification of the receptor or ligand? Could there have been something wrong with my inputs?
>>
>> Input:
>>
>> Input file for running PB and GB
>> &general
>> interval=5, startframe=250, endframe= 1250
>> /
>> &pb
>> istrng=0.150,radiopt=0,indi=4.0
>> /
>>
>>
>>
>> Sincerely,
>>
>> Peter Ramdhan
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Received on Tue Jan 30 2024 - 01:00:02 PST
