Re: [gmx-users] Invalid Order for Directive Defaults Error Due to Force Field Mixing
Thanks Dr. Justin, Got it -Amir On Fri, Mar 3, 2017 at 5:00 AM, Justin Lemkul 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 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
Re: [gmx-users] Invalid Order for Directive Defaults Error Due to Force Field Mixing
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 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.
Re: [gmx-users] Invalid Order for Directive Defaults Error Due to Force Field Mixing
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? Thanks -Amir On Thu, Mar 2, 2017 at 2:10 PM, Justin Lemkul 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. > -- 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.
Re: [gmx-users] Invalid Order for Directive Defaults Error Due to Force Field Mixing
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.
[gmx-users] Invalid Order for Directive Defaults Error Due to Force Field Mixing
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! 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 -- 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.
