[AMBER] mmpbsa: PB Bomb in pb_aaradi()

From: Wei Chen <cwbluesky.gmail.com>
Date: Wed, 10 Sep 2014 17:18:53 -0400


I am using AmberTools14 for MMPBSA calculation. The force field is ff12SB.

My input for pb is:
   istrng=0.15, prbrad=1.4, radiopt=1, inp=2,
   indi=1.0, exdi=80.0, sander_apbs=0, scale=2.0,
   cavity_surften=0.0378, cavity_offset=-0.5692

I got this error:
"PB Bomb in pb_aaradi(): No radius assigned for atom 7 CB 2C".

It is a CB atom in a standard amino acid. I saw somebody asked the same
question before. The program cannot recognized the atom type "2C". I think
many people are using ff12SB force field now. I wonder why regular atom
types in ff12SB cannot be recognized. Is that because the optimized radii
set obtained by using other force field, thus not suitable for ff12SB?

Thank you!

Wei Chen
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Received on Wed Sep 10 2014 - 14:30:02 PDT
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