[gmx-users] CGenFF generated prm/itp overriding and messing with charmm36-nov2016.ff?

Justin Lemkul jalemkul at vt.edu
Thu Mar 2 23:07:35 CET 2017

On 3/2/17 3:17 PM, Jonathan Saboury wrote:
> Hello all,
> I'm trying to run a simulation of 2DRD in water with charmm36-nov2016.ff
> (AcrB co complexed with minocycline). The main problem I'm having is
> generating an .itp of minocycline (getting it from a reference would not
> work for me as I need to simulate other small organic molecules not in
> literature). I have run md on 2drd not complexed successfully with the same
> methodology.
> I've tried charmm-gui and that worked but that was messy as I needed to
> include two forcefields:
> ./charmm36-nov2016.ff/forcefield.itp and charmm36.itp. This proceeded to
> overriding Bond parameters. What parameters were overridden and the effect
> of that I have no idea (hopefully you can enlighten me).

If you are building a system with CHARMM-GUI, you should not make any changes 
whatsoever to the topology it gives you.  The reason is that what CHARMM-GUI 
does is extract only the necessary subset of the CHARMM force field that is 
relevant to your system and put it in an all-included topology.  This is 
different from the "normal" GROMACS approach of constructing a whole force field 
and then using a subset of it.

> So I tried CGenFF. This generated the itp (along with a prm) with the ff I
> wanted was used, no other ff was included (yay!).
> However, this led to a "overriding Bond parameters" as well as a number of
> coordinates in coordinate file (complex_b4_ion.pdb, 410866) does not match
> topology (topol.top, 434665) error. I'm fairly sure my .top file includes
> everything correctly, so I'm thinking that somehow this .prm/.itp messed up
> with original ff and added some atoms. Or did I do something very stupid?
> Terminal IO: http://pastebin.com/raw/KY6SRtdm
> topol.top: http://pastebin.com/raw/fKJfpr6a
> Whole folder download (10.9 MB): http://www.filedropper.com/2drdtar

The errors suggest you enabled the option to include all relevant force field 
parameters in the resulting stream file.  This will cause overlap with the 
existing force field, which is not what you want.


> Thank you for the help, I really appreciate it :-)
> - Jonathan


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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