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

Jonathan Saboury jsabou1 at gmail.com
Thu Mar 2 23:55:56 CET 2017

Dear Justin

Do you mean the "Include parameters that are already in CGenFF" option? I
didn't tick that option but I did have to tick "guess bond orders from
connectivity" or else it would error because of hypervalent carbon (5

Screen shot: http://oi65.tinypic.com/2h5tqfs.jpg


- Jonathan

On Thu, Mar 2, 2017 at 2:07 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

> 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.
> -Justin
> 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
> http://mackerell.umaryland.edu/~jalemkul
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