Hi Amber
I have some questions regarding calculating G using MMPBSA:
1. My system is just a peptide. Is it possible that I do not need a ligand
for my MMPASA calculation if I would like to compare the G with different
conformations? (I clustered a few conformers and would like to compare
them) .
2. Is it correct that my command is as follows?
$MMPBSA.py -O -i mmpbsa.in -o mmpbsa.out -cp 14sb_1.prmtop -y 1us_14sb.dcd
> mmpbsa_calculation.out &
or I should include -rp and -lp using the same complex_protom, although I
don't have ligand in my system.
3. Can I use .dcd instead of .mdcrd for my calculation?
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Received on Sat Jul 27 2019 - 10:30:03 PDT
