[gmx-users] pdb2gmx generates very large .top for lipids with charmm36-nov2016.ff

Jonathan Saboury jsabou1 at gmail.com
Mon Mar 13 01:36:34 CET 2017

Hello all,

I generated a 3:1 POPE:POPG bilayer with charmm-gui, ran the minimization,
equilibration, and production runs given. Then I copied the 10ns production
run .gro to a different folder so that I can run it with
charmm36-nov2016.ff instead of the ff given.

When running the command "gmx_mpi pdb2gmx -ff charmm36-nov2016 -f
old_membrane_lipid_only.pdb -o old_membrane_pdb2gmx.pdb -p topol.top -water
tip3p" it generates a very large .top file (26.8 MB) that has [ atoms ] and
perhaps other headings.

I was under the impression that the .top should have been small and just
contained the include line for where the POPE and POPG .itps were in the
charmm36-nov2016. Did I do something wrong? Would this give me a simulation
that isn't accurate?

Command Notes: http://pastebin.com/raw/TC0L1H4K
topol.top (26.8 MB): https://ufile.io/5897d2

Thank you again for all your help, it is very much appreciated :)

- Jonathan

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