What version of Amber are you using?
On Sat, Aug 2, 2014 at 2:40 AM, Nadia Li <amber.nadiali.gmail.com> wrote:
> Dear amber users,
>
> I am trying to calculate MMGB/PBSA. Using the same prmtop files, my mmgbsa
> worked successfully, but the mmpbsa failed with CalcError: mmpbsa_py_energy
> failed with prmtop complex.prmtop.
>
> I ran again with "use_sander=1", still having the problem, but the mdout
> gave:
> PB Bomb in pb_aaradi(): No radius assigned for atom 7 CB 2C
> I saw a thread suggesting to set "inp=1, radiopt=0" in &pb, but not working
> for me.
>
> The following is the input file I used.
>
>
>
>
>
>
>
> *&general startframe=1,endframe=149,interval=10,verbose=1,
> use_sander=1,/&pb istrng=0.0,inp=1,radiopt=0, /*
>
> I have run MMPBSA on different MD systems, but keeping having this problem,
> while my MMGBSA all worked.
> It will be much appreciated if anyone can help me with this? Thank you in
> advance!
>
> Regards,
> Nadia
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>
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Sat Aug 02 2014 - 05:30:02 PDT
