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

[Justin Lemkul]

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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