Re: [gmx-users] Implicit solvent model in Gromacs
On Mon, Jan 23, 2012 at 10:01 AM, Gianluca Interlandi gianl...@u.washington.edu wrote: Dear gromacs users list, I noticed that gromacs can perform simulations with an implicit solvent model using a GBSA method. Is it compatible with the CHARMM22 force field? look for gbsa.itp showed amber03.ff/forcefield.itp amber03.ff/gbsa.itp amber94.ff/forcefield.itp amber94.ff/gbsa.itp amber96.ff/forcefield.itp amber96.ff/gbsa.itp amber99.ff/forcefield.itp amber99.ff/gbsa.itp amber99sb.ff/forcefield.itp amber99sb.ff/gbsa.itp amber99sb-ildn.ff/forcefield.itp amber99sb-ildn.ff/gbsa.itp amberGS.ff/forcefield.itp amberGS.ff/gbsa.itp oplsaa.ff/forcefield.itp oplsaa.ff/gbsa.itp seems not. Thanks, Gianluca - Gianluca Interlandi, PhD gianl...@u.washington.edu +1 (206) 685 4435 http://artemide.bioeng.washington.edu/ Postdoc at the Department of Bioengineering at the University of Washington, Seattle WA U.S.A. - -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Implicit solvent model in Gromacs
lina wrote: On Mon, Jan 23, 2012 at 10:01 AM, Gianluca Interlandi gianl...@u.washington.edu wrote: Dear gromacs users list, I noticed that gromacs can perform simulations with an implicit solvent model using a GBSA method. Is it compatible with the CHARMM22 force field? look for gbsa.itp showed amber03.ff/forcefield.itp amber03.ff/gbsa.itp amber94.ff/forcefield.itp amber94.ff/gbsa.itp amber96.ff/forcefield.itp amber96.ff/gbsa.itp amber99.ff/forcefield.itp amber99.ff/gbsa.itp amber99sb.ff/forcefield.itp amber99sb.ff/gbsa.itp amber99sb-ildn.ff/forcefield.itp amber99sb-ildn.ff/gbsa.itp amberGS.ff/forcefield.itp amberGS.ff/gbsa.itp oplsaa.ff/forcefield.itp oplsaa.ff/gbsa.itp seems not. It's called gb.itp in the charmm27.ff subdirectory. -Justin Thanks, Gianluca - Gianluca Interlandi, PhD gianl...@u.washington.edu +1 (206) 685 4435 http://artemide.bioeng.washington.edu/ Postdoc at the Department of Bioengineering at the University of Washington, Seattle WA U.S.A. - -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Implicit solvent model in Gromacs
On Tue, Jan 24, 2012 at 12:08 AM, Justin A. Lemkul jalem...@vt.edu wrote: lina wrote: On Mon, Jan 23, 2012 at 10:01 AM, Gianluca Interlandi gianl...@u.washington.edu wrote: Dear gromacs users list, I noticed that gromacs can perform simulations with an implicit solvent model using a GBSA method. Is it compatible with the CHARMM22 force field? look for gbsa.itp showed amber03.ff/forcefield.itp amber03.ff/gbsa.itp amber94.ff/forcefield.itp amber94.ff/gbsa.itp amber96.ff/forcefield.itp amber96.ff/gbsa.itp amber99.ff/forcefield.itp amber99.ff/gbsa.itp amber99sb.ff/forcefield.itp amber99sb.ff/gbsa.itp amber99sb-ildn.ff/forcefield.itp amber99sb-ildn.ff/gbsa.itp amberGS.ff/forcefield.itp amberGS.ff/gbsa.itp oplsaa.ff/forcefield.itp oplsaa.ff/gbsa.itp seems not. It's called gb.itp in the charmm27.ff subdirectory. Thanks. your information is very helpful. I know the answer asked on another thread. -Justin Thanks, Gianluca - Gianluca Interlandi, PhD gianl...@u.washington.edu +1 (206) 685 4435 http://artemide.bioeng.washington.edu/ Postdoc at the Department of Bioengineering at the University of Washington, Seattle WA U.S.A. - -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Implicit solvent model in Gromacs
Dear gromacs users list, I noticed that gromacs can perform simulations with an implicit solvent model using a GBSA method. Is it compatible with the CHARMM22 force field? Thanks, Gianluca - Gianluca Interlandi, PhD gianl...@u.washington.edu +1 (206) 685 4435 http://artemide.bioeng.washington.edu/ Postdoc at the Department of Bioengineering at the University of Washington, Seattle WA U.S.A. - -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Implicit solvent model in Gromacs
On 23/01/2012 1:01 PM, Gianluca Interlandi wrote: Dear gromacs users list, I noticed that gromacs can perform simulations with an implicit solvent model using a GBSA method. Is it compatible with the CHARMM22 force field? Thanks, Gianluca - Gianluca Interlandi, PhD gianl...@u.washington.edu +1 (206) 685 4435 http://artemide.bioeng.washington.edu/ Postdoc at the Department of Bioengineering at the University of Washington, Seattle WA U.S.A. - Yes, see ref 110 of the manual. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
