[AMBER] Issue with MM/PBSA calculations on membrane system

From: Gilberto Pereira <gilberto.pereiraportugal.gmail.com>
Date: Mon, 23 Aug 2021 16:57:06 +0200

Dear members of the Amber mailing list.

I am trying to carry out some MM/PBSA calculations in a protein-ligand
system whose simulation included a POPC membrane and explicit solvent,
carried out using GROMACS and converted to Amber format with GROMBER. The
water and membrane atoms were removed previous to the MM/PBSA calculation.
Below is the input file used to setup up the MM/PBSA run using AmberTools18.

Sample input file for MMPBSA with membrane proteins
startframe=1000, endframe=2000, interval=100,
keep_files=1, debug_printlevel=2
radiopt=0, indi=4.0, istrng=0.150, exdi=80.0,
fillratio=1.25, ipb=1, nfocus=1,
bcopt=10, eneopt=1, cutfd=7.0, cutnb=99.0,
npbverb=1, solvopt=2, inp=1,
memopt=1, emem=1.0, mctrdz=90.31, mthick=46, poretype=1,
maxarcdot=15000, sasopt=0,
Upon submission of the calculation, the program crashes with the following

minimizing coord set # 1
PB bomb in pb_atmlist(): MAXNEI too short

Could you please help me to solve this issue?

Best regards,
Gilberto Pereira
AMBER mailing list
Received on Mon Aug 23 2021 - 08:00:02 PDT
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