Just to 'close' this thread:
I failed to see that K* (i.e. K<wildcard>) is in the default strip-mask,
and this caught the non-standard residue in this case.
Defining a 'user' stripmask solved the 'problem' as it should.
Apologies!
Marc
On 8 June 2017 at 07:42, Marc van der Kamp <marcvanderkamp.gmail.com> wrote:
> 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
>>
>
>
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Received on Mon Jun 12 2017 - 05:00:04 PDT
