On Wed, Jun 24, 2015 at 4:02 AM, Muthukumaran R <kumaran.bicpu.edu.in>
wrote:
> I tried MMPBSA, with following input on amber tools 14 (AMBER12)
>
>
>
> Sample input file with pb analysis
>
> &general
>
> startframe=15000, endframe=20000,interval=50,
>
> verbose=2, keep_files=1,
>
> /
>
> &pb
>
> istrng=0.1, indi=4, scale=2, inp=2,
>
> /
>
> when I included the option "ipb=1" in &general or &pb, it gives the same
> error
>
> InputError: Unknown variable ipb in &pb.
>
​MMPBSA.py makes no use of the ipb variable. It is automatically set to 1
in the sander or mmpbsa_py_energy input files. If you want to change this
value to something *besides* 1, you probably need to set use_sander=1 and
then use the -make-mdins and -use-mdins flags to modify the sander mdin
files directly. If the value of 1 suffices (as it usually does), just omit
ipb altogether.
For pure energies, I don't think the value of ipb will make much of a
difference. If you're doing dynamics with PB, then the functional form of
the dielectric boundary matters since you're computing gradients. But if
you're just computing solvation free energies, I doubt it will have a very
noticeable effect (hopefully someone can correct me if I'm misunderstanding
this).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Jun 24 2015 - 05:30:03 PDT
