On Mon, Jun 5, 2017 at 10:35 AM, Marc van der Kamp <marcvanderkamp.gmail.com
> wrote:
> Dear Amber list,
>
> This is quite a naive question (as I don't usually use MMPBSA.py) - but I
> am struggling with how to run MMPBSA.py with a protein-ligand system in
> which I also have a non-standard residue in the protein.
>
> I've generated topology files and trajectory files containing the complex
> (without solvent), the protein/receptor only (with non-standard residue)
> and the ligand only.
>
> The trouble is that - according to the manual - I can only specify a
> solvated trajectory file, a receptor one and a ligand one. The complex
> trajectory is thus generated by MMPBSA.py,
Where does it say this in the manual? You need to specify all of those
topology files, including the complex. If you omit the solvated prmtop,
the input trajectory will be assumed to be already stripped of solvent and
ions. If you omit both the receptor and ligand topology files, it will be
assumed you only want a "stability" calculation (energies of a single
species).
> BUT this does not include the
> non-standard amino acid (it is not present in _MMPBSA_complex.mdcrd.0 or
> _MMPBSA_complex.pdb)
>
MMPBSA.py does not handle custom residues in any special way. However, if
your custom residue has a name equal to one of the ions in the default
"strip_mask" variable
(:WAT,Cl*,CIO,Cs+,IB,K*,Li+,MG*,Na+,Rb+,CS,RB,NA,F,CL) then that would
explain why your residue got deleted from the complex. In that case,
either pre-strip your input trajectories or set `strip_mask` to another
value that does not include your custom residue name.
HTH,
Jason
--
Jason M. Swails
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jun 07 2017 - 21:00:02 PDT
