Dear all,
I have two questions:
a) I have run several (~200 ns) simulations, using the restart file from
the end of one simulation as a starting point for next simulation. So in
total, I have a total of 1 microsecond. But the problem is I was able to
combine coordinate files from each individual simulation run for up to~
750ns. If I try to combine anything above this in cpptraj, the process is
killed automatically at around 70% completion and the final output is never
generated. Is this because the file is too big? Is there a way to get
around this? I did:
parm x.prmtop
trajin Prod1.mdcrd
trajin Prod2.mdcrd
........................
.......
..............
trajout final.mdcrd
b) I have a multimeric protein complex with proteins a,b,c, and d. I wanted
to use MMGBSA and calculate dG between protein a and b. The simulation is
run with the whole four-protein complex. When I use ambpdb before
simulation to prepare for simulation, amber automatically numbers from top
to bottom starting with 1. But the protein a'' and 'b' is dimer 'a' is
attached to 'c' and 'b' is attached to 'd'. So ideally I would like to make
'ac' and 'bd' and submit them for dG calculation. When I did 'a' and 'bcd'
for the dG calculation, I get a really high number and I am not sure if I
am doing this right. What is the best way to approach this?
Thank you in advance,
Sincerely,
Jag
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Received on Wed Feb 21 2018 - 12:30:02 PST
