Dear Jason or others,
Thank you for your reply.
On 8 June 2017 at 04:55, Jason Swails <jason.swails.gmail.com> wrote:
> 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).
>
>
Sorry for not being clear before:
I do indeed specify all those *topology* files. The problem is with the
*trajectory* files generated. Even though the topology files for the
complex and the receptor contain the non-standard residue (which has
residue name KPI, thus not one of the ion names in the default strip mask),
the *trajectory* files do not - which is why MMPBSA.py appears to fail.
The example command I specified (where strip.solvated.top is the
complex.top file):
$AMBERHOME/bin/MMPBSA.py -O -sp solvated.top -i mmgbsa.i -cp
strip.solvated.top -rp receptor.top -lp ligand.top -y md.crd -yr rec.nc -yl
lig.nc &
Many thanks,
Marc
>
> > 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
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jun 08 2017 - 00:00:02 PDT
