Jason,
apologies for getting back to you on this again.
I’ve run the script. The terminal output is shown here:
Shouldn’t there be a complex.prmtop produced as well? According to the help file, one should also get a prmtop of the stripped complex.
$ ante-mmpbsa.py -p 4fqt_solv.prmtop -c complex.prmtop -r receptor.prmtop -l ligand.prmtop -n :126 --radii=mbondi2
Creating receptor topology file by stripping :126 from 4fqt_solv.prmtop
Done creating receptor topology file!
Creating ligand topology file by stripping !(:126) from 4fqt_solv.prmtop
Done creating ligand topology file!
Thanks once again
George
On 26Feb, 2015, at 2:21 PM, Jason Swails <jason.swails.gmail.com> wrote:
> On Thu, 2015-02-26 at 14:16 -0300, George Tzotzos wrote:
>> Jason,
>>
>> Many thanks for the prompt and very helpful reply.
>>
>> I’m interested in option 4: lB -- sA.sB and lA -- sA.lB.sB
>>
>> I had a quick look at ante-MMPBSA.py help. As I’ve never used the
>> script before I’d be grateful for one additional clarification.
>>
>> Given the above option and that ligand lA is residue 126 of my current
>> topology:
>>
>> 1. Is the following script correct?
>>
>> -p lA.sA.lB.sB_solv.prmtop -c lA.sA.lB.sB.prmtop -r sA.lB.sB.prmtop
>> -l lA.prmtop -s :126 -n :126 --radii=mbondi2
>
> No. -s/--strip-mask is the mask of atoms that you want to delete to go
> from lA.sA.lB.sB_solv.prmtop --> lA.sA.lB.sB.prmtop. It serves the same
> function as strip_mask in MMPBSA.py's input file.
>
> So assuming you don't need to set strip_mask in MMPBSA.py, just take out
> "-s :126".
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
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Received on Thu Feb 26 2015 - 10:30:03 PST
