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From: Jag Silwal <jagsilwal.gmail.com>
Sent: 25 June 2017 17:15:15
To: AMBER Mailing List
Subject: [AMBER] mbondi set up
Dear all,
I just have a very trivial question. I just finished 200 ns simulation in
my protein complex. But just when running MMGBSA, I realized that while
saving the initial topology and coordinate files for everything, I forgot
to set PBRadii mbondi. (I usually use "set default PBRadii mbondi3" just
before saving solvated and non solvated topologies and coordinates). I
completely missed this command in tleap. I came to realize this when
prmtop failure message popped out during MMGBSA run.
Now my question is do I need to re-run the entire simulation from the
scratch (with mbondi) or can I simply create a new topology file with
mbondi and use these to already ran simulation to do further analyses? As
far as I understand, mbondi and igb are parameters for GB/SA run. I
recreated the topology files using mbondi and I didn't get any errors
while calculating MMGBSA.
I just wanted to be 100% on this before I do anything with this.
