Re: [gmx-users] pdb2gmx handle the dna structure containing potassium
On 5/10/17 4:16 AM, Changdong LIU wrote: Dear GROMACS users, I used pdb2gmx to generate topology file for the g_quadruplex DNA which constains 3 potassiums. If the 3 potassiums were deleted ,the pdb2gma successfully generated the topology file for DNA. But failed when the 3 potassiums were added into the pdb file. The topol.top is like: ; Include forcefield parameters #include "amber99sb-ildn.ff/forcefield.itp" ; Include chain topologies #include "topol_DNA_chain_C.itp" #include "topol_Ion_chain_D.itp" ; Include water topology #include "amber99sb-ildn.ff/spce.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include "amber99sb-ildn.ff/ions.itp" [ system ] ; Name --- [ molecules ] ; Compound#mols DNA_chain_C 1 Ion_chain_D 1 It seems that pdb2gmx could not recognize both dna and potassiums. As the potassium is necessary for the stability of the DNA g_quadruplex, would you please give any suggestions how to generated the topology file containing the ions? Make sure you're using a decent force field, e.g. see extensive work by Sponer and others about all the nasty defects in existing force fields for GQ simulations. Spoiler alert: none of them do a great job. But an old AMBER FF like AMBER99 is surely a poor choice. -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] pdb2gmx handle the dna structure containing potassium
Take a look at you pdb file. May be potassium atom is defined as HETATM in pdb. amber99sb-ildn ff has K in its ions.itp file. On Wed, May 10, 2017 at 1:46 PM, Changdong LIU wrote: > Dear GROMACS users, > > > I used pdb2gmx to generate topology file for the g_quadruplex DNA which > constains 3 potassiums. > > > If the 3 potassiums were deleted ,the pdb2gma successfully generated the > topology file for DNA. > > > But failed when the 3 potassiums were added into the pdb file. The > topol.top is like: > > > ; Include forcefield parameters > #include "amber99sb-ildn.ff/forcefield.itp" > > ; Include chain topologies > #include "topol_DNA_chain_C.itp" > #include "topol_Ion_chain_D.itp" > > ; Include water topology > #include "amber99sb-ildn.ff/spce.itp" > > #ifdef POSRES_WATER > ; Position restraint for each water oxygen > [ position_restraints ] > ; i funct fcxfcyfcz >11 1000 1000 1000 > #endif > > ; Include topology for ions > #include "amber99sb-ildn.ff/ions.itp" > > [ system ] > ; Name > --- > > [ molecules ] > ; Compound#mols > DNA_chain_C 1 > Ion_chain_D 1 > > > It seems that pdb2gmx could not recognize both dna and potassiums. > > As the potassium is necessary for the stability of the DNA g_quadruplex, > would you please give any suggestions how to generated the topology file > containing the ions? > > Thanks. > > > Best > > Changdong > > > -- > 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.
[gmx-users] pdb2gmx handle the dna structure containing potassium
Dear GROMACS users, I used pdb2gmx to generate topology file for the g_quadruplex DNA which constains 3 potassiums. If the 3 potassiums were deleted ,the pdb2gma successfully generated the topology file for DNA. But failed when the 3 potassiums were added into the pdb file. The topol.top is like: ; Include forcefield parameters #include "amber99sb-ildn.ff/forcefield.itp" ; Include chain topologies #include "topol_DNA_chain_C.itp" #include "topol_Ion_chain_D.itp" ; Include water topology #include "amber99sb-ildn.ff/spce.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include "amber99sb-ildn.ff/ions.itp" [ system ] ; Name --- [ molecules ] ; Compound#mols DNA_chain_C 1 Ion_chain_D 1 It seems that pdb2gmx could not recognize both dna and potassiums. As the potassium is necessary for the stability of the DNA g_quadruplex, would you please give any suggestions how to generated the topology file containing the ions? Thanks. Best Changdong -- 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.
