Re: [gmx-users] atom name - topology
How about exclusions - I want to exclude all non-bonded parameters within this one residue made of 2500 atoms. Would: [ moleculetype ] ; Namenrexcl N 2500 Solve the problem? Or shall I create [ exclusions ] part ? Which one would be faster in terms of performance? Steven On Thu, Dec 5, 2013 at 1:41 PM, Steven Neumann wrote: > Thank you > > > On Thu, Dec 5, 2013 at 1:25 PM, Justin Lemkul wrote: > >> >> >> On 12/5/13 5:18 AM, Steven Neumann wrote: >> >>> I have not tried as wish to know before loosing time on making the >>> topology. So each atom column needs letters - whats the maximum number of >>> letters? Can I name them with same names (its one residue) as well as in >>> pdb? >>> >>> >> The easiest thing to do is define each residue as if it were a polymer, >> then you don't have to worry about 2500+ unique atom names. If each unit >> is only a few beads, this becomes trivial to do and pdb2gmx will do all the >> work via .rtp entry. >> >> -Justin >> >> >> Steven >>> >>> >>> On Wed, Dec 4, 2013 at 5:37 PM, Justin Lemkul wrote: >>> >>> On 12/4/13 11:48 AM, Steven Neumann wrote: Dear Gmx Users, > > My molecule contains 2516 atoms made of 5 type of beads: BAS, POL, NON, > ACI, GLY and I want to create a topology. Is it possible to make one > residue of one [ moleculetype ] with this number of atoms so that: > > [ moleculetype ] > ; Namenrexcl > MOL3 > > [ atoms ] > ; nr type resnr residue atom cgnr charge mass > typeBchargeB massB > ; residue 1 1N rtp 1N q 0.0 > 1BAS11N110133.208 > 2POL11N22087.08 > 3NON11N330147.172 > 4BAS11N440157.204 > 5POL11N55087.08 > ... > 2500 POL11N25005087.08 > > Can atom column contain number from 1 to 2500? > > > Have you tried it? Are you getting some problem? IIRC the atom column requires a string (name), not an integer. That's what the atom number column is for. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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. >> Postdoctoral Fellow >> >> Department of Pharmaceutical Sciences >> School of Pharmacy >> Health Sciences Facility II, Room 601 >> University of Maryland, Baltimore >> 20 Penn St. >> Baltimore, MD 21201 >> >> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >> >> == >> -- >> 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] atom name - topology
Thank you On Thu, Dec 5, 2013 at 1:25 PM, Justin Lemkul wrote: > > > On 12/5/13 5:18 AM, Steven Neumann wrote: > >> I have not tried as wish to know before loosing time on making the >> topology. So each atom column needs letters - whats the maximum number of >> letters? Can I name them with same names (its one residue) as well as in >> pdb? >> >> > The easiest thing to do is define each residue as if it were a polymer, > then you don't have to worry about 2500+ unique atom names. If each unit > is only a few beads, this becomes trivial to do and pdb2gmx will do all the > work via .rtp entry. > > -Justin > > > Steven >> >> >> On Wed, Dec 4, 2013 at 5:37 PM, Justin Lemkul wrote: >> >> >>> >>> On 12/4/13 11:48 AM, Steven Neumann wrote: >>> >>> Dear Gmx Users, My molecule contains 2516 atoms made of 5 type of beads: BAS, POL, NON, ACI, GLY and I want to create a topology. Is it possible to make one residue of one [ moleculetype ] with this number of atoms so that: [ moleculetype ] ; Namenrexcl MOL3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeBchargeB massB ; residue 1 1N rtp 1N q 0.0 1BAS11N110133.208 2POL11N22087.08 3NON11N330147.172 4BAS11N440157.204 5POL11N55087.08 ... 2500 POL11N25005087.08 Can atom column contain number from 1 to 2500? Have you tried it? Are you getting some problem? IIRC the atom column >>> requires a string (name), not an integer. That's what the atom number >>> column is for. >>> >>> -Justin >>> >>> -- >>> == >>> >>> Justin A. Lemkul, Ph.D. >>> Postdoctoral Fellow >>> >>> Department of Pharmaceutical Sciences >>> School of Pharmacy >>> Health Sciences Facility II, Room 601 >>> University of Maryland, Baltimore >>> 20 Penn St. >>> Baltimore, MD 21201 >>> >>> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >>> >>> == >>> -- >>> 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. > Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > == > -- > 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] atom name - topology
On 12/5/13 5:18 AM, Steven Neumann wrote: I have not tried as wish to know before loosing time on making the topology. So each atom column needs letters - whats the maximum number of letters? Can I name them with same names (its one residue) as well as in pdb? The easiest thing to do is define each residue as if it were a polymer, then you don't have to worry about 2500+ unique atom names. If each unit is only a few beads, this becomes trivial to do and pdb2gmx will do all the work via .rtp entry. -Justin Steven On Wed, Dec 4, 2013 at 5:37 PM, Justin Lemkul wrote: On 12/4/13 11:48 AM, Steven Neumann wrote: Dear Gmx Users, My molecule contains 2516 atoms made of 5 type of beads: BAS, POL, NON, ACI, GLY and I want to create a topology. Is it possible to make one residue of one [ moleculetype ] with this number of atoms so that: [ moleculetype ] ; Namenrexcl MOL3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeBchargeB massB ; residue 1 1N rtp 1N q 0.0 1BAS11N110133.208 2POL11N22087.08 3NON11N330147.172 4BAS11N440157.204 5POL11N55087.08 ... 2500 POL11N25005087.08 Can atom column contain number from 1 to 2500? Have you tried it? Are you getting some problem? IIRC the atom column requires a string (name), not an integer. That's what the atom number column is for. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] atom name - topology
I have not tried as wish to know before loosing time on making the topology. So each atom column needs letters - whats the maximum number of letters? Can I name them with same names (its one residue) as well as in pdb? Steven On Wed, Dec 4, 2013 at 5:37 PM, Justin Lemkul wrote: > > > On 12/4/13 11:48 AM, Steven Neumann wrote: > >> Dear Gmx Users, >> >> My molecule contains 2516 atoms made of 5 type of beads: BAS, POL, NON, >> ACI, GLY and I want to create a topology. Is it possible to make one >> residue of one [ moleculetype ] with this number of atoms so that: >> >> [ moleculetype ] >> ; Namenrexcl >> MOL3 >> >> [ atoms ] >> ; nr type resnr residue atom cgnr charge mass >> typeBchargeB massB >> ; residue 1 1N rtp 1N q 0.0 >> 1BAS11N110133.208 >> 2POL11N22087.08 >> 3NON11N330147.172 >> 4BAS11N440157.204 >> 5POL11N55087.08 >> ... >> 2500 POL11N25005087.08 >> >> Can atom column contain number from 1 to 2500? >> >> > Have you tried it? Are you getting some problem? IIRC the atom column > requires a string (name), not an integer. That's what the atom number > column is for. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > == > -- > 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] atom name - topology
On 12/4/13 11:48 AM, Steven Neumann wrote: Dear Gmx Users, My molecule contains 2516 atoms made of 5 type of beads: BAS, POL, NON, ACI, GLY and I want to create a topology. Is it possible to make one residue of one [ moleculetype ] with this number of atoms so that: [ moleculetype ] ; Namenrexcl MOL3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeBchargeB massB ; residue 1 1N rtp 1N q 0.0 1BAS11N110133.208 2POL11N22087.08 3NON11N330147.172 4BAS11N440157.204 5POL11N55087.08 ... 2500 POL11N25005087.08 Can atom column contain number from 1 to 2500? Have you tried it? Are you getting some problem? IIRC the atom column requires a string (name), not an integer. That's what the atom number column is for. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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.
