On Tue, Mar 19, 2013 at 1:22 PM, Vivek Shankar Bharadwaj <
vbharadw.mymail.mines.edu> wrote:
> Hi Amber users,
>
> I am attempting to do mmgbsa binding energy calculations on a multi-subunit
> protein system. I am using ante-mmpbsa.py for creating the complex,
> receptor and ligand topology files. The system has 1629 amino acid residues
> with 1 ligand.
>
> When I specify the ligand resid ID I get the following error...
>
> Creating ligand topology file by stripping !(:2495) from complex.prmtop
> Error: Creating ligand topology failed!
> Loaded Amber topology file complex.prmtop
> Reading input from STDIN...
> > Removing mask '!(:2495)' (69614 atoms) from the topology file.
> IndexError: list index out of range
>
The only way I get this error is if I strip atom in the system. Does your
system have just 69614 atoms? If so, then :2495 is _not_ your ligand
residue number (note, if you want atom number you need to use .2495).
You can use ParmEd and the "printDetails" command to test out various atom
masks to make sure that the mask you use selects the atoms you want to
select.
When used correctly, ante-MMPBSA.py should work for any system.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Mar 19 2013 - 13:30:03 PDT
