[gmx-users] Position restraint for ions
Hi! I was wondering if there is any clear way to create position restraints for ions. I am using: *g_select -s rna_ions.gro -n index.ndx -on rna_ion.ndx -select 'group non-Water'* - to create an index for my RNA and Ions; and: *genrestr -f rna_ions.gro -n rna_ion.ndx -o rna_ion.itp -fc 800 800 800* - to create an .itp file for them. I am also including this new .itp file to the topology using the proper 'ifdef' statements, but I get this when I run grompp: *Fatal error:[ file rna_ion.itp, line 1753 ]:Atom index (90849) in position_restraints out of bounds (1-1748).This probably means that you have inserted topology section position_restraintsin a part belonging to a different molecule than you intended to.In that case move the position_restraints section to the right molecule.* It seems the ions are not included as the same moleculetype as the RNA and Gromacs see this as an error. Would someone knows a neat way to do this? Cheers! -- Marcelo Depólo Polêto Student of MSc Cell and Molecular Biology - UFRGS (Brazil) B.Sc. Biochemistry - University of Viçosa (Brazil) -- 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] Position restraint for ions
On 4/14/15 1:48 PM, Marcelo Depólo wrote: Hi! I was wondering if there is any clear way to create position restraints for ions. I am using: *g_select -s rna_ions.gro -n index.ndx -on rna_ion.ndx -select 'group non-Water'* - to create an index for my RNA and Ions; and: *genrestr -f rna_ions.gro -n rna_ion.ndx -o rna_ion.itp -fc 800 800 800* - to create an .itp file for them. I am also including this new .itp file to the topology using the proper 'ifdef' statements, but I get this when I run grompp: *Fatal error:[ file rna_ion.itp, line 1753 ]:Atom index (90849) in position_restraints out of bounds (1-1748).This probably means that you have inserted topology section position_restraintsin a part belonging to a different molecule than you intended to.In that case move the position_restraints section to the right molecule.* It seems the ions are not included as the same moleculetype as the RNA and Gromacs see this as an error. Would someone knows a neat way to do this? The ions need to be merged into the RNA [moleculetype] definition in order for this to work. This isn't something that is done after the fact with index groups as you're trying above; the topologies need to be merged, e.g. with pdb2gmx -chainsep -merge, or by hand if the ions aren't part of the input coordinate file. -Justin -- == 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] Position restraint for ions
*Fatal error:[ file rna_ion.itp, line 1753 ]:Atom index (90849) in position_restraints out of bounds (1-1748).This probably means that you have inserted topology section position_restraintsin a part belonging to a different molecule than you intended to.In that case move the position_restraints section to the right molecule.* It seems the ions are not included as the same moleculetype as the RNA and Gromacs see this as an error. Would someone knows a neat way to do this? The ions need to be merged into the RNA [moleculetype] definition in order for this to work. This isn't something that is done after the fact with index groups as you're trying above; the topologies need to be merged, e.g. with pdb2gmx -chainsep -merge, or by hand if the ions aren't part of the input coordinate file. Thanks, Justin. I have tried that by using '-merge all' but this created a .top without the ions. RNA and water only. grompp even warned me that my system now has non-zero charge. Any ideas? And surprisingly, if I remove the water with 'editconf', and only then I merge them using pdb2gmx, then the topology is written right (with the ions and zero net charge). Confusing, han? -Justin -- == 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 -- Marcelo Depólo Polêto Student of MSc Cell and Molecular Biology - UFRGS (Brazil) B.Sc. Biochemistry - University of Viçosa (Brazil) -- 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] Position restraint for ions
2015-04-14 14:54 GMT-03:00 Justin Lemkul jalem...@vt.edu: On 4/14/15 1:48 PM, Marcelo Depólo wrote: Hi! I was wondering if there is any clear way to create position restraints for ions. I am using: *g_select -s rna_ions.gro -n index.ndx -on rna_ion.ndx -select 'group non-Water'* - to create an index for my RNA and Ions; and: *genrestr -f rna_ions.gro -n rna_ion.ndx -o rna_ion.itp -fc 800 800 800* - to create an .itp file for them. I am also including this new .itp file to the topology using the proper 'ifdef' statements, but I get this when I run grompp: *Fatal error:[ file rna_ion.itp, line 1753 ]:Atom index (90849) in position_restraints out of bounds (1-1748).This probably means that you have inserted topology section position_restraintsin a part belonging to a different molecule than you intended to.In that case move the position_restraints section to the right molecule.* It seems the ions are not included as the same moleculetype as the RNA and Gromacs see this as an error. Would someone knows a neat way to do this? The ions need to be merged into the RNA [moleculetype] definition in order for this to work. This isn't something that is done after the fact with index groups as you're trying above; the topologies need to be merged, e.g. with pdb2gmx -chainsep -merge, or by hand if the ions aren't part of the input coordinate file. Thanks, Justin. I have tried that by using '-merge all' but this created a .top without the ions. RNA and water only. grompp even warned me that my system now has non-zero charge. Any ideas? -Justin -- == 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. -- Marcelo Depólo Polêto Student of MSc Cell and Molecular Biology - UFRGS (Brazil) B.Sc. Biochemistry - University of Viçosa (Brazil) -- 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] Position restraint for ions
On 4/14/15 3:25 PM, Marcelo Depólo wrote: *Fatal error:[ file rna_ion.itp, line 1753 ]:Atom index (90849) in position_restraints out of bounds (1-1748).This probably means that you have inserted topology section position_restraintsin a part belonging to a different molecule than you intended to.In that case move the position_restraints section to the right molecule.* It seems the ions are not included as the same moleculetype as the RNA and Gromacs see this as an error. Would someone knows a neat way to do this? The ions need to be merged into the RNA [moleculetype] definition in order for this to work. This isn't something that is done after the fact with index groups as you're trying above; the topologies need to be merged, e.g. with pdb2gmx -chainsep -merge, or by hand if the ions aren't part of the input coordinate file. Thanks, Justin. I have tried that by using '-merge all' but this created a .top without the ions. RNA and water only. grompp even warned me that my system now has non-zero charge. Any ideas? And surprisingly, if I remove the water with 'editconf', and only then I merge them using pdb2gmx, then the topology is written right (with the ions and zero net charge). Confusing, han? I can offer no rationalization without seeing your commands and perhaps getting access to your files. Merging RNA+ions is something I do routinely, but I always do that before adding any water or anything else. -Justin -- == 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] Position restraint for ions
2015-04-14 17:26 GMT-03:00 Justin Lemkul jalem...@vt.edu On 4/14/15 3:25 PM, Marcelo Depólo wrote: *Fatal error:[ file rna_ion.itp, line 1753 ]:Atom index (90849) in position_restraints out of bounds (1-1748).This probably means that you have inserted topology section position_restraintsin a part belonging to a different molecule than you intended to.In that case move the position_restraints section to the right molecule.* It seems the ions are not included as the same moleculetype as the RNA and Gromacs see this as an error. Would someone knows a neat way to do this? The ions need to be merged into the RNA [moleculetype] definition in order for this to work. This isn't something that is done after the fact with index groups as you're trying above; the topologies need to be merged, e.g. with pdb2gmx -chainsep -merge, or by hand if the ions aren't part of the input coordinate file. Thanks, Justin. I have tried that by using '-merge all' but this created a .top without the ions. RNA and water only. grompp even warned me that my system now has non-zero charge. Any ideas? And surprisingly, if I remove the water with 'editconf', and only then I merge them using pdb2gmx, then the topology is written right (with the ions and zero net charge). Confusing, han? I can offer no rationalization without seeing your commands and perhaps getting access to your files. Merging RNA+ions is something I do routinely, but I always do that before adding any water or anything else. So how do you insert your ions without water to be exchanged for the ions? -Justin -- == 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. -- Marcelo Depólo Polêto Student of MSc Cell and Molecular Biology - UFRGS (Brazil) B.Sc. Biochemistry - University of Viçosa (Brazil) -- 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] Position restraint for ions
On 4/14/15 4:50 PM, Marcelo Depólo wrote: 2015-04-14 17:26 GMT-03:00 Justin Lemkul jalem...@vt.edu On 4/14/15 3:25 PM, Marcelo Depólo wrote: *Fatal error:[ file rna_ion.itp, line 1753 ]:Atom index (90849) in position_restraints out of bounds (1-1748).This probably means that you have inserted topology section position_restraintsin a part belonging to a different molecule than you intended to.In that case move the position_restraints section to the right molecule.* It seems the ions are not included as the same moleculetype as the RNA and Gromacs see this as an error. Would someone knows a neat way to do this? The ions need to be merged into the RNA [moleculetype] definition in order for this to work. This isn't something that is done after the fact with index groups as you're trying above; the topologies need to be merged, e.g. with pdb2gmx -chainsep -merge, or by hand if the ions aren't part of the input coordinate file. Thanks, Justin. I have tried that by using '-merge all' but this created a .top without the ions. RNA and water only. grompp even warned me that my system now has non-zero charge. Any ideas? And surprisingly, if I remove the water with 'editconf', and only then I merge them using pdb2gmx, then the topology is written right (with the ions and zero net charge). Confusing, han? I can offer no rationalization without seeing your commands and perhaps getting access to your files. Merging RNA+ions is something I do routinely, but I always do that before adding any water or anything else. So how do you insert your ions without water to be exchanged for the ions? I don't restraint bulk ions. I'm only interested in structurally bound ions, and there are various reasons to restrain those during different processes. Why do you want to restrain bulk ions? You should be able to do whatever you like, but without more information I can't diagnose what's happening in your case. -Justin -- == 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.
