Hello,
I have finished a constant ph simulation and I am trying to use pbsa to get the electrostatic potential.
I am running the command pbsa -O -i pbsa.mdin -o pbsa.mdout -p complex.parm7 -c prod.nc
The pbsa.mdin file is as follow:
Sample PB visualization input
&cntrl
inp=0
/
&pb
npbverb=1, space=1., sasopt=2,
phiout=1, phiform=2
/
It gave an error in the bottom of the pbsa.mdout file: PB Bomb in pb_aaradi(): No radius assigned for atom 11777 EPW EP
I saw a similar question in the mailing list, and they said to set inp=1 and radiopt=0, so I tried the following pbsa.mdin:
Sample PB visualization input
&cntrl
inp=1
/
&pb
npbverb=1, space=1., sasopt=2,
phiout=1, phiform=2,
radiopt=0
/
But it gave the error:
Fortran runtime error: Bad value during floating point read
Error termination. Backtrace:
#0 0x7ffff6221e18 in formatted_transfer_scalar_read
at /usr/local/pace-apps/spack/root/releases/v0.18/stage/fliu67/spack-stage-gcc-10.3.0-o57x6h2gubo7bzh7evmy4mvibdqrlghr/spack-src/libgfortran/io/transfer.c:1650
#1 0x7ffff62235d3 in formatted_transfer
at /usr/local/pace-apps/spack/root/releases/v0.18/stage/fliu67/spack-stage-gcc-10.3.0-o57x6h2gubo7bzh7evmy4mvibdqrlghr/spack-src/libgfortran/io/transfer.c:2339
#2 0x4166d3 in ???
#3 0x4054cd in ???
#4 0x407834 in ???
#5 0x40787a in ???
#6 0x7ffff57c0554 in ???
#7 0x40201d in ???
#8 0xffffffffffffffff in ???
Any guidance would be greatly appreciated!
Thanks!
Zoey
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Received on Fri Jan 05 2024 - 12:00:03 PST
