[AMBER] MMPBSA prmtop problem

From: Nadia Li <amber.nadiali.gmail.com>
Date: Fri, 1 Aug 2014 23:40:59 -0700

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
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

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Received on Sat Aug 02 2014 - 00:00:02 PDT
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