Wei,
Try setting radiopt=0 in the input file. It looks like you have an atom
(2C?) that doesn't either doesn't have a radii assigned to it normally, or
is named something that MMPBSA doesn't recognize. Having radiopt=0 will
have MMPBSA use the prmtop to provide the radii and should fix your problem.
Best,
Kenneth
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
>
--
Ask yourselves, all of you, what power would hell have if those imprisoned
here could not dream of heaven?
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Apr 21 2015 - 10:30:03 PDT
