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

From: George Tzotzos <gtzotzos.me.com>
Date: Mon, 16 Mar 2015 16:12:44 -0300

Thank you Jason and Kenneth

I used Kennethís script to get topologies stripped of waters and ligands (Case 2). parminfo shows the prmtop files to be as expected. When I run
MMPBSA.py.MPI, it throws the following error
CalcError: /Users/3i521409/Programs/amber12/bin/cpptraj failed with prmtop subA.prmtop!
Error occured on rank 9.
Exiting. All files have been retained.
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 9

Is there a way to troubleshoot this?

Thanks again for the help

George

On 16Mar, 2015, at 3:37 PM, Jason Swails <jason.swails.gmail.com> wrote:

> On Mon, 2015-03-16 at 14:26 -0300, George Tzotzos wrote:
>> 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
>
> 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
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber

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Received on Mon Mar 16 2015 - 12:30:02 PDT
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