Re: [gmx-users] CHARMM36 format POPC
Thanks a lot Peter. Will try out with this. -Anirban On Wed, May 2, 2012 at 9:42 PM, Peter C. Lai wrote: > http://uab.hyperfine.info/~pcl/files/popc36/ > > These were generated for the following work: (please reference): > Lai, P.C. and Crasto, C.J. > Beyond Modeling: All-Atom Olfactory Receptor Model Simulations > Front. Gene. > Volume 3 Year 2012 Number 61 > DOI: 10.3389/fgene.2012.00061 > > On 2012-05-02 05:49:17PM +0530, Anirban Ghosh wrote: > > Hi ALL, > > > > I was looking for a CHARMM36 format (atom-types) equilibrated POPC > bilayer > > (PDB/GRO) to use with the CHARMM36 FF in GROAMCS 4.5.5. I downloaded one > > from Dr. Klauda's site ( > > http://terpconnect.umd.edu/~jbklauda/research/download.html), but that > > popc.pdb (under CHARMM36 FF) seem to have different atom-types (like P1 > in > > place of P, etc.) and hence pdb2gmx throws up error when processed with > > CHARMM36 FF option. Is there any CHARMM36 FF format equilibrated POPC > > bilayer available online, or can someone provide, please? > > Thanks a lot in advance. > > > > > > Regards, > > > > Anirban > > > -- > > 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 > > > -- > == > Peter C. Lai| University of Alabama-Birmingham > Programmer/Analyst | KAUL 752A > Genetics, Div. of Research | 705 South 20th Street > p...@uab.edu | Birmingham AL 35294-4461 > (205) 690-0808 | > == > > -- > 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 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] CHARMM36 format POPC
http://uab.hyperfine.info/~pcl/files/popc36/ These were generated for the following work: (please reference): Lai, P.C. and Crasto, C.J. Beyond Modeling: All-Atom Olfactory Receptor Model Simulations Front. Gene. Volume 3 Year 2012 Number 61 DOI: 10.3389/fgene.2012.00061 On 2012-05-02 05:49:17PM +0530, Anirban Ghosh wrote: > Hi ALL, > > I was looking for a CHARMM36 format (atom-types) equilibrated POPC bilayer > (PDB/GRO) to use with the CHARMM36 FF in GROAMCS 4.5.5. I downloaded one > from Dr. Klauda's site ( > http://terpconnect.umd.edu/~jbklauda/research/download.html), but that > popc.pdb (under CHARMM36 FF) seem to have different atom-types (like P1 in > place of P, etc.) and hence pdb2gmx throws up error when processed with > CHARMM36 FF option. Is there any CHARMM36 FF format equilibrated POPC > bilayer available online, or can someone provide, please? > Thanks a lot in advance. > > > Regards, > > Anirban > -- > 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 -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu| Birmingham AL 35294-4461 (205) 690-0808 | == -- 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] CHARMM36 format POPC
Hi ALL, I was looking for a CHARMM36 format (atom-types) equilibrated POPC bilayer (PDB/GRO) to use with the CHARMM36 FF in GROAMCS 4.5.5. I downloaded one from Dr. Klauda's site ( http://terpconnect.umd.edu/~jbklauda/research/download.html), but that popc.pdb (under CHARMM36 FF) seem to have different atom-types (like P1 in place of P, etc.) and hence pdb2gmx throws up error when processed with CHARMM36 FF option. Is there any CHARMM36 FF format equilibrated POPC bilayer available online, or can someone provide, please? Thanks a lot in advance. Regards, Anirban -- 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
