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

Fri Mar 3 07:58:36 CET 2017

Hi,

PDB has a well defined fixed-width field format:
http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM
so only columns 13-16 can contain the atom name. By eye, it looks like the
cgenff python script gets this wrong, using 14-17 (but do check in the
actual files). If so, please report that to them to get it fixed.

Fortunately, you can fix the file to move the space in column 13 to column
18 pretty easily, eg with the Unix cut and paste command line tools.

Mark

On Fri, 3 Mar 2017 05:28 Jonathan Saboury <jsabou1 at gmail.com> wrote:

> I think I narrowed it down to the problem. This time I only simulated MIY
> in water and the problem occurs in gmx solvate and gmx grompp
>
> gmx solvate seems to only reads a max of 3 chars for atom type/number (not
> sure the correct name, it is the 3rd entry in pdb). This results in the
> output pdb invalid if the atom type/name has 3+ chars (4 in the case of the
> cgenff generated itps.
>
> Here is the comparison below:
> terminal IO: http://pastebin.com/raw/Vzibp4U0
> miy_b4_solv.pdb: http://pastebin.com/raw/CG8S3scz
> miy_b4_ion.pdb: http://pastebin.com/raw/1StxheeJ
>
> Fixing the atom types does not solve this problem however (grompp still
> only reading 3 chars?).
> So either gmx solvate/grompp  needs to fix their atom type reading or
> cgenff needs to fix their atom naming?
>
> Just wanted to confirm this is the correct assessment of the  problem with
> you before proceeding to ask for changes :)
>
> Thanks as always!
>
> - Jonathan
>
> On Thu, Mar 2, 2017 at 2:57 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
> >
> >
> > On 3/2/17 5:55 PM, Jonathan Saboury wrote:
> >
> >> 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
> >> bonds)
> >>
> >>
> > Yeah, that's the box.  The only way I can think of to get overriding
> > parameters is to include things that are already present in the force
> field.
> >
> > -Justin
> >
> > Screen shot: http://oi65.tinypic.com/2h5tqfs.jpg
> >>
> >> Thanks!
> >>
> >> - Jonathan
> >> <http://oi65.tinypic.com/2h5tqfs.jpg>
> >>
> >>
> >>
> >>
> >> 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
> >>>
> >>> ==================================================
> >>> --
> >>> Gromacs Users mailing list
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> >>>
> >>>
> > --
> > ==================================================
> >
> > 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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