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

Justin Lemkul jalemkul at vt.edu
Mon Mar 13 01:59:47 CET 2017

On 3/12/17 8:36 PM, Jonathan Saboury wrote:
> 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.

Why?  The topology CHARMM-GUI gives you still works, and that's sort of the 
purpose - it gives you everything you need for the system.

> 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?

No, because pdb2gmx will generate an explicit copy of the topology for every 
instance of every residue, which leads to an extremely redundant topology with 
many copies of lipids and water.  As stated above, there is no need to 
re-generate your topology.  Use what CHARMM-GUI gives you.  We worked hard to 
make it easy for the end user :)



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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