Thanks Dr. Justin, Got it
-Amir On Fri, Mar 3, 2017 at 5:00 AM, Justin Lemkul <jalem...@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 <jalem...@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 >>> >>> jalem...@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 >>> /Mailing_Lists/GMX-Users_List before posting! >>> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> * For (un)subscribe requests visit >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>> send a mail to gmx-users-requ...@gromacs.org. >>> >>> > -- > ================================================== > > 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 > > jalem...@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 > /Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.