On Mon, 2015-03-16 at 14:26 -0300, George Tzotzos 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
Actually, this is the shell assigning special meaning to the bang (!)
character. If you want to use it as a character in a command-line, you
need to enclose that particular argument in quotations so the shell
knows not to invoke its special meaning:
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
>
> 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
This has to do with atoms and residues getting 'renumbered' following
the strip_mask. When you delete residue number 126, the residue that
*was* 127 in the solvated complex is 126 in the stripped complex (from
which the ligand and receptor files are generated). Kenneth's
suggestion is the best approach to dodge this renumbering issue
completely.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Mar 16 2015 - 12:00:02 PDT
