[gmx-users] Invalid Order for Directive Defaults Error Due to Force Field Mixing

[Amir Zeb]

Thanks Dr. Justin,

Got it

-Amir

On Fri, Mar 3, 2017 at 5:00 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 3/3/17 1:49 AM, Amir Zeb wrote:
>
>> Hi Dr. Justin,
>>
>> I'm wondering that you have mentioned CHARMm27 is not a valid identifier
>> of
>> protein forcefield, but we have so many articles already published while
>> using CHARMm27 ff. Can you please let us know how to trace this
>> unsuitability of CHARMm27 especially for protein-ligand simulation?
>>
>>
> I have said nothing about the suitability of the force field; it's
> perfectly fine to use (though I think more modern versions, e.g. C36 and
> C36m are generally preferable).
>
> I'm really just being pedantic and trying to prevent more errors from
> entering the literature.  There is no such thing as a "CHARMM27 protein
> force field."  It gets lumped into "CHARMM27" based solely on file naming.
> The parameters in GROMACS that are labeled "charmm27.ff" are actually
> CHARMM22/CMAP with various revisions that have appeared in the literature
> over several years before CHARMM36 was released.  So anyone claiming to use
> "CHARMM27" as their protein force field is using a misnomer.  For the sake
> of accuracy, I am trying to encourage people to break this habit and use
> the proper name of the force field.
>
> Just because it's published, doesn't mean it's right :)
>
> -Justin
>
>
> Thanks
>>
>> -Amir
>>
>> On Thu, Mar 2, 2017 at 2:10 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>>
>>> On 3/2/17 2:16 PM, Sanim Rahman wrote:
>>>
>>> Hi all,
>>>>
>>>> I am attempting to run a membrane protein simulation where I am
>>>> describing
>>>> my protein and solvent in terms of CHARMM27 and my lipids in CHARMM36.
>>>> When
>>>> I use the grompp command, I get the following error:
>>>>
>>>> Fatal error:
>>>> Syntax error - File forcefield.itp, line 9
>>>> Last line read:
>>>> '[ defaults ]'
>>>> Invalid order for directive defaults
>>>>
>>>> To create my topology file, I took my protein.top and at the bottom
>>>> included my lipid.itp and solvent.itp. The error is referencing to my
>>>> charmm36 force field file. I was unsure what to do so I just removed the
>>>> line with [ defaults ] on it and tried running it again. This time I
>>>> received this error:
>>>>
>>>> Fatal error:
>>>> Syntax error - File ffnonbonded.itp, line 5
>>>> Last line read:
>>>> '[ atomtypes ]'
>>>> Invalid order for directive atomtypes
>>>>
>>>> Is the source of the error from how my topology files are processing the
>>>> force field files since I am using both CHARMM27 and CHARMM36? I read a
>>>> previous thread that you can't have two [ default ] lines which make
>>>> sense
>>>> but I am unsure of what is the proper protocol to get around this to
>>>> include both force fields. Any help will be deeply appreciated!
>>>>
>>>>
>>>> I mentioned this last week in another thread, but I'll say it again:
>>> "CHARMM27" is not a valid identifier for a protein force field.  What
>>> you're trying to use is CHARMM22/CMAP.
>>>
>>> The bigger question is why you want to use this combination?  It may not
>>> be practical or possible to do so in GROMACS.  You'll likely have to hack
>>> out the bonded and nonbonded parameters that relate to proteins and marry
>>> them together with the lipid-only portions of CHARMM36.
>>>
>>> -Justin
>>>
>>> Thank You,
>>>
>>>>
>>>> *Sanim Rahman*
>>>> B.S. Chemical Engineering, 2019
>>>> Resident Assistant, Castor Hall Engineering Living Learning Community
>>>> 2016-2017
>>>> Co-Founder and Co-President of the Undergraduate Research Society
>>>> Undergraduate Researcher, Global Center for Hearing and Speech Research
>>>>
>>>>
>>>> --
>>> ==================================================
>>>
>>> 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
>
> ==================================================
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> Gromacs Users mailing list
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