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

Fri Mar 3 14:02:35 CET 2017

On 3/2/17 11:28 PM, Jonathan Saboury 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 :)
>

I don't follow.  How does the spacing of atom names (note: there are not "types" 
in a coordinate file, that's a topological construct) affect the contents of the 
generated .str/.itp file?

If we've got a bug in our conversion script, I'm happy to fix it.  I just need 
to know what I'm fixing.

-Justin

> 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
>>>>
>>>> ==================================================
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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
>>
>> ==================================================
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support
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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

==================================================