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-- Michael F. Crowley, Ph.D. Principal Scientist, Biomolecular Sciences Division National Renewable Energy Laboratory 1617 Cole Blvd. Golden, CO 80401 303-384-6345 office 303-887-0149 cell On 1/31/12 10:44 AM, "George Tzotzos" <gtzotzos.me.com> wrote: >Hi Dwight > >Following your very useful suggestions, I have two additional queries. > >1. Since you selected specific atoms in your receptor mask, what >criterion did you use to define the initial distance (r2) between the >ligand and the receptor? > >2. What criterion did you use to define rk2 which I assume is in >kcal/mol-A^2 . Isn't the value (=500.0) on the high side? > >With thanks > > >George. > > > > >On Jan 25, 2012, at 3:06 AM, Dwight McGee wrote: > >> Hi George, >> >> If you are trying to identify pathways, then it is better to use a >>center >> of mass restraint like you stated. I have attached an example of how I >>have >> specified it for my system. The flag "igr1" is the mask for the atoms in >> the receptor, where I only chose "CA" atoms for the mask. I am not sure >> what protein you are performing steered molecular dynamics on, but if >>there >> are such things as flaps that lie over the active site, then you will >>not >> want to include those in the "igr1" mask. The flag "igr2" signifies >>atoms >> belonging to the ligand in which I only included the heavy atoms; the >> hydrogens were not included. >> >> On Tue, Jan 24, 2012 at 8:40 AM, George Tzotzos <gtzotzos.me.com> wrote: >> >>> Hi everybody, >>> >>> I'm a complete novice in this and I'm trying to follow the Manual. >>> >>> In summary, I'm trying to identify receptor tunnel(s) through which a >>> ligand can be released from the binding pocket. >>> >>> I'm using the restraint and input files attached at the end of this >>> message. >>> >>> As can be seen from the .rst file, I'm changing the restraint between >>> atoms. I have a feeling that this is wrong. Wouldn't it be better to >>>use >>> something like a distant restraint between the centre of mass of the >>> protein and the ligand? If so, how can one define these centres? In >>>this >>> case, I assume that the iat variable would have to be changed. To what? >>> >>> A second question relates to the directionality of the "push"? Is there >>> one? Should one repeat the simulation using different atoms within the >>> binding pocket of the protein? >>> >>> Apologies if these questions are naive but I need to start from >>>somewhere >>> and I'm not at all familiar with restraints applied in NMR. >>> >>> Thanks in advance for any help >>> >>> George >>> ====================== >>> dist.RST >>> # Change distance restraint between atoms >>> &rst iat=1533,2223, r2=4.492, rk2=14.0, r2a=18.0 / >>> #1533 (protein atom); 2223 (ligand atom) >>> >>> smd.in >>> smd 2wc6-bombykol >>> &cntrl >>> imin=0,irest=1,ntx=5, >>> nstlim=1000,dt=0.002, >>> ntc=2,ntf=2, >>> cut=8.0, ntb=2, ntp=1, taup=2.0, >>> ntpr=1, ntwx=1, ntwr=1, >>> ntt=3, gamma_ln=2.0, ig=-1, >>> temp0=300.0, >>> jar=1, >>> / >>> &wt TYPE='DUMPFREQ', istep1=1, / >>> &wt TYPE='END', / >>> DISANG=dist.RST >>> DUMPAVE=dist_vs_t >>> LISTIN=POUT >>> LISTOUT=POUT >>> >>> >>> _______________________________________________ >>> AMBER mailing list >>> AMBER.ambermd.org >>> http://lists.ambermd.org/mailman/listinfo/amber >>> >> >> >> >> -- >> T. Dwight McGee Jr. >> Quantum Theory Project >> University of Florida >> Graduate Student >> dwight.mcgee.gmail.com >> >> "Problems cannot be solved at the same level of awareness that created >> them." >> Albert Einstein >> <dist.RST.nfv.mut.orig>_______________________________________________ >> AMBER mailing list >> AMBER.ambermd.org >> http://lists.ambermd.org/mailman/listinfo/amber > >_______________________________________________ >AMBER mailing list >AMBER.ambermd.org >http://lists.ambermd.org/mailman/listinfo/amber