On 2012-04-16 10:14:01AM -0700, Shima Arasteh wrote: > So, I can not use the coordinates of the output files of gromos runs. Right?
You can but you may need to rename the atoms for each residue for pdb2gmx to work. > > > ________________________________ > From: Peter C. Lai <[email protected]> > To: Discussion list for GROMACS users <[email protected]> > Sent: Monday, April 16, 2012 8:23 PM > Subject: Re: [gmx-users] GROMOS87 and CHARMM27 > > On 2012-04-16 08:26:00AM -0700, Shima Arasteh wrote: > > Dear GROMACS users, > > > > I reproduced the results of a protein-membrane system by using force field > > GROMOSE87. This protein forms ion channel in membrane. > > Now if I wanna study the ion conduction through this channel using force > > field CHARMM27 in umbrella sampling method, is it possible? Can I use the > > results of the system simulation which has been derived by GROMOS87? > > By definition, switching to a different forcefield like that usually requires > the regeneration of the system's topology, so your new system will be > different from your old one anyway. In addition, you may need to rename the > atoms in the coordinate files obtained from previous gromos runs to match > those in the charmm27 residue files. > > -- > ================================================================== > Peter C. Lai | University of Alabama-Birmingham > Programmer/Analyst | KAUL 752A > Genetics, Div. of Research | 705 South 20th Street > [email protected] | Birmingham AL 35294-4461 > (205) 690-0808 | > ================================================================== > > -- > gmx-users mailing list [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- > gmx-users mailing list [email protected] > 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 [email protected]. > 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 [email protected] | Birmingham AL 35294-4461 (205) 690-0808 | ================================================================== -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
