I second Kenneth's suggestion. The only way to get radiopt to work
"correctly" is to modify the PBSA source code and add support for the atom
types in the new force fields yourself. To my knowledge, the radiopt radii
have not been kept up-to-date with the latest versions of the Amber force
field, so your options are the following:
1. Modify the PBSA source code to recognize the new atom types in whichever
force field you are using
2. Use ff99SB instead, since those are the atom types that (I believe) were
originally supported by radiopt
3. Use radiopt=0 and simply take the solvation radii from the prmtop
I would opt for (3), since those are pretty good in my experience.
As for inp=2 vs. inp=1 -- which one is "better" is still an open question.
It's been my experience that inp=1 is more reliable, although some people
have reported better results with inp=2 in their studies.
Note that if you are using the latest version of MMPBSA.py, the -make-mdins
and -use-mdins route is unnecessary for controlling inp=2 and radiopt --
those can be set directly in the MMPBSA.py input file.
HTH,
Jason
On Tue, Apr 21, 2015 at 11:28 AM, wliu <wliu.itcs.ecnu.edu.cn> wrote:
> Hello, everyone,
>
> I'm learning MMPBSA.py recently, for the sake of calculating the
> binding free energy of protein with an organic molecule. Though
> AmberTools13 Reference Manual, to make the calculation more accurate, I
> choose INP=2 (which is default, and I have use -make-mdins option to
> check the temporary mdin files) to decompose non-polar solvation energy
> into cavity and dispersion terms. In the meanwhile, I need to set
> radiopt=1. My input file is written as:
>
> Input file for running PB and GB
> &general
> startframe=0, endframe=600, interval=10,
> verbose =2,
> # entropy =1,
> strip_mask=:WAT:Na+
> /
> &gb
> igb=5, saltcon=0.100
> /
> &pb
> radiopt=1,
> istrng=0.100,
> indi =1,
> /
>
> and I get the error information as:
>
> CalcError: /gpfs01/home/ymei/software/amber14/bin/mmpbsa_py_energy
> failed with prmtop com_nobox.prmtop!
> PB Bomb in pb_aaradi(): No radius assigned for atom 7 CB
> 2C
>
> Exiting. All files have been retained.
>
> In addition, I did a test, no matter the ligand is a protein or an
> organic molecule, and both in MMPBSA.py and mm_pbsa.pl, this error will
> occur. Can anyone tell me what this error information stand for and how
> to use radiopt = 1 correctly?
> I would be appreciate for the helps!
>
> Sincerely yours,
> Wei Liu，
>
> wliu.itcs.ecnu.edu.cn
> East China Normal University
> ShangHai，china，200062
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Apr 21 2015 - 11:00:07 PDT
