Dear all,
Can someone please reply to this query
On Thu, May 21, 2020 at 1:39 PM Prasanth G, Research Scholar <
prasanthghanta.sssihl.edu.in> wrote:
> Dear all,
>
> I am interested in carrying out per residue free energy decomposition for
> a protein - ligand complex.
>
> The residue code of my ligand is 671.
> a) Is there a way to specify in the command (mmpbsa.in file) to run
> decomposition analysis of the residues that are 4 angstroms around the
> ligand?
>
> b) Would it take the same time to decompose the values for all the
> residues?
>
> c) Is there a way to incorporate these values into a pdb file for
> visualization? For example,
> mmpbsa_perresidue.png
> <https://drive.google.com/a/sssihl.edu.in/file/d/11SMwbtrJ31xyqxINqACEujqmmXozY2zo/view?usp=drive_web>
>
> d) I had neutralized the system with counter ions and did not saturate the
> system with any more salt. would this script look correct for mmpbsa, in
> this case?
> ----
> Input file for running PB and GB
> &general
> endframe=50, verbose=2,
> keep_files=1,
> full_traj=1,
> netcdf=1,
> entropy=0,
> /
> &gb
> igb=5,
> /
> &pb
> inp=1,
> radiopt=0,
> /
> -----
> Thank you in advance.
>
> --
> Regards,
> Prasanth.
>
--
Regards,
Prasanth.
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Received on Sat May 23 2020 - 00:00:02 PDT
