George,
Each subunit consists of 125 residues (subA residues 1-125, subB residues:
> 127-151), the ligands residues are 126 and 152 and the conserved waters
> residues 253 and 254.
>
I'm confused by the numbering of your atoms- shouldn't subB be 127-251, and
the second ligand at 252? You may want to double check, since that's what
could be throwing it off.
But you can try-
ante-mmpbsa.py -p complex_solv.prmtop -c subA-subB.prmtop -r subA.prmtop -l
subB.prmtop -s :WAT,:Na+ -n :1-126,:253 --radii=mbondi2
Which should give you the subunits with the ligands and water molecules,
assuming that 253 is the corresponding water for the first subunit. I can't
speak for the syntax error, though.
For the second case, which looks like you want both dimers without their
respective water molecules and ligands? If so, you can try-
ante-mmpbsa.py -p complex_solv.prmtop -c subA-subB.prmtop -r subA.prmtop -l
subB.prmtop -s :WAT,:Na+,:126,:252,:253-254 -n :1-125 --radii=mbondi2
Best,
Kenneth
On Mon, Mar 16, 2015 at 1:26 PM, George Tzotzos <gtzotzos.me.com> wrote:
> I’m working on a homodimer that includes two identical ligands (one per
> subunit) as well as two conserved water molecules.
>
> Each subunit consists of 125 residues (subA residues 1-125, subB residues:
> 127-151), the ligands residues are 126 and 152 and the conserved waters
> residues 253 and 254.
>
> CASE 1.
>
> I’m using the following ante-mmpbsa script to generate topology files:
>
> ante-mmpbsa.py -p complex_solv.prmtop -c subA-subB.prmtop -r subA.prmtop
> -l subB.prmtop -s :WAT,Na+,&!:253-254 -n :127-252,254 --radii=mbondi2
>
> Apparently the syntax of the strip mask -s :WAT,Na+,&!:253-254 is wrong
> and the error message given is -bash: :253-254: bad word specifier
>
> CASE 2.
>
> Script
>
> ante-mmpbsa.py -p complex_solv.prmtop -c subA-subB.prmtop -r subA.prmtop
> -l subB.prmtop -s :WAT,Na+,:126,:152 -n :127-251 --radii=mbondi2
>
> Also same as above but modifying the mask of the above to: -s
> :WAT,Na+,:126,152
>
> produced topologies the same topologies: (a) subA-subB containing 250
> residues, 4 molecules; (b) subA containing 126 residues, 2 molecules; (c)
> subB containing 124 residues, 3 molecules
>
> Any suggestions on correcting this would be most helpful
>
> Regards
>
> George
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Ask yourselves, all of you, what power would hell have if those imprisoned
here could not dream of heaven?
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Mar 16 2015 - 11:30:03 PDT
