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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jan 24 2024 - 12:00:02 PST
