Re: [gmx-users] Reg dimers
Thanks a lot Justin On Mon, Jul 9, 2012 at 7:21 PM, Justin A. Lemkul wrote: > > > On 7/9/12 9:48 AM, Ramya LN wrote: >> >> Dear all, >> I have done protein-ligand dynamics.I got the final gro file.When >> converted to PDB, i observed that my active site has ligand but two >> chains of teh protein got separated. What might be the reason for >> this?should i consider this as an error in my simulation???kindly help >> me in this regard. >> > > http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions > > -Justin > > -- > > > Justin A. Lemkul, Ph.D. > Research Scientist > 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 > * Only plain text messages are allowed! > * 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 -- Ramya -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Reg dimers
On 7/9/12 9:48 AM, Ramya LN wrote: Dear all, I have done protein-ligand dynamics.I got the final gro file.When converted to PDB, i observed that my active site has ligand but two chains of teh protein got separated. What might be the reason for this?should i consider this as an error in my simulation???kindly help me in this regard. http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 * Only plain text messages are allowed! * 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] Reg dimers
Dear all, I have done protein-ligand dynamics.I got the final gro file.When converted to PDB, i observed that my active site has ligand but two chains of teh protein got separated. What might be the reason for this?should i consider this as an error in my simulation???kindly help me in this regard. Thanks -- Ramya -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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
