[AMBER] ante-mmpbsa.py: problem with the mask syntax

From: George Tzotzos <gtzotzos.me.com>
Date: Mon, 16 Mar 2015 14:26:16 -0300

Iím 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.

Iím 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




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Received on Mon Mar 16 2015 - 10:30:03 PDT
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