Aw: [gmx-users] Force Field for peptides and proteins

2013-08-13 Thread lloyd riggs
.  In addition, difference in simply looking at domain changes in proteins or affinites, etc...   Gesendet: Montag, 12. August 2013 um 14:19 Uhr Von: "Maria Astón Serrano" An: gmx-users@gromacs.org Betreff: [gmx-users] Force Field for peptides and proteins Dear Gromacs users, We would like t

Re: [gmx-users] Force Field for peptides and proteins

2013-08-12 Thread rajat desikan
On this note, I wanted to ask about simulated unfolding of proteins. I have a primarily alpha-helical-protein ( about 300 amino acids, 5 alpha helices, no beta strands) and 3 of its single point mutants. Now, to answer the question of relative stability, I want to place them in a water bath and hea

Re: [gmx-users] Force Field for peptides and proteins

2013-08-12 Thread Justin Lemkul
On 8/12/13 8:19 AM, Maria Astón Serrano wrote: Dear Gromacs users, We would like to know which is the Force Field which is customarily preferred for simulations of peptides and proteins. Interestingly, this same question was just asked on the development list, although the discussion indee

Re: [gmx-users] Force Field for peptides and proteins

2013-08-12 Thread Dr. Vitaly Chaban
I like CHARMM. Dr. Vitaly V. Chaban On Mon, Aug 12, 2013 at 2:19 PM, Maria Astón Serrano < m.aston.serr...@gmail.com> wrote: > Dear Gromacs users, > > We would like to know which is the Force Field which is customarily > preferred for simulations of peptides and proteins. > > Thank you very muc

Re: [gmx-users] Force Field for peptides and proteins

2013-08-12 Thread Kieu Thu Nguyen
It depends on what properties of peptides and proteins that you want to explore. ~Thu On Mon, Aug 12, 2013 at 7:19 PM, Maria Astón Serrano < m.aston.serr...@gmail.com> wrote: > Dear Gromacs users, > > We would like to know which is the Force Field which is customarily > preferred for simulation

[gmx-users] Force Field for peptides and proteins

2013-08-12 Thread Maria Astón Serrano
Dear Gromacs users, We would like to know which is the Force Field which is customarily preferred for simulations of peptides and proteins. Thank you very much. Best regards, Maria -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please s