Custom Search
-- Thank you, B. Sangeetha On Thu, Dec 6, 2012 at 3:18 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote: > Hi, > > 'atomicfluct' is best used following an RMS-fit to an averaged > structure. Assuming you want local fluctuations for each chain, and > since you have several chains, you should probably rms-fit and > calculate fluctuations for each one separately (unless you want some > sort of global fluctuation for the entire system). The best procedure > in my opinion is to run your calculation in two phases, one in which > the coords are stripped and imaged, the second in which you perform > the actual calc. The easiest way to do this IMHO is with cpptraj since > the 'autoimage' command takes a lot of the guesswork out of imaging. > Note that in your case since you have ions in-between your chains that > the atom numbering of the system will be altered after the strip > command (i.e. the second chain will start at residue 211 instead of > 213 since the two intervening ions will be stripped). The following > examples assume you are using cpptraj: > > 1) strip and image the trajectory, calculate the average structure: > > parm protein.prmtop > trajin md1.mdcrd 1 500 1 > - > - > - > trajin md50.mdcrd 1 500 1 > strip :WAT,Cl- outprefix strip > average chain1.pdb :1-210 pdb > average chain2.pdb :211-420 pdb > average chain3.pdb :421-630 pdb > trajout strip.md.nc netcdf > > After this you will have a stripped topology 'strip.protein.prmtop' > that corresponds to the stripped traj 'strip.md.nc' and 3 PDB files > containing the average structure of each chain. > > 2) rms fit to average structure, calculate atomic fluctuations: > > parm strip.protein.prmtop > trajin strip.md.nc > parm chain1.pdb > reference chain1.pdb parm chain1.pdb [chain1] > parm chain2.pdb > reference chain2.pdb parm chain2.pdb [chain2] > parm chain3.pdb > reference chain3.pdb parm chain2.pdb [chain2] > rms ref [chain1] :1-210 :1-210 > atomicfluct out chain1.fluct.dat :1-210.CA byatom > rms ref [chain2] :211-420 :1-210 > atomicfluct out chain2.fluct.dat :211-420.CA byatom > rms ref [chain3] :421-630 :1-210 > atomicfluct out chain3.fluct.dat :421-630.CA byatom > > Note this is intended as a guideline only - since I don't have access > to your system I can only guess at the best way to go about > calculating things. Hopefully this is somewhat helpful. Good luck! > > -Dan > > On Fri, Nov 30, 2012 at 7:16 AM, Sangeetha B <sangeetha.bicpu.edu.in> > wrote: > > Dear amber users, > > > > I am simulating a trimeric protein a with flexible C-terminal region for > 50 > > ns. Each chain is 210 aa in length. Residues 211 and 212 are two > structural > > Cl- ions. > > I am having imaging issues while extracting the structures and performing > > any analysis. I have extracted pdb structures with different image center > > options. > > Without any imaging, the chains are separated in different directions and > > with different options, the location of these chains vary. > > > > I went through the amber mailing list and with the its help, I finally > > found the image commands shown below gave reasonably good structures when > > visualized. > > Whereas, when I use this for analyzing the RMS fluctuations very strange > > behavior is seen. > > > > The ptraj script that I use for generating RMS fluctuation is as follows: > > > > trajin md1.mdcrd 1 500 1 > > - > > - > > - > > trajin md50.mdcrd 1 500 1 > > strip :WAT,Cl- > > center :1-210 mass > > image :1-210 bymask :1-210 > > center :1-423 mass > > image :1-423 bymask :1-423 > > center :1-632 mass > > image :1-632 bymask :1-632 > > image origin center > > atomicfluct out rmsf_md50ns.out .CA byatom > > > > > > When I plot the output from this script (rmsf_with_imaging.jpg) there is > a > > sudden increase in fluctuation at the beginning of the second chain which > > starts at 213. > > But when I don't use any imaging commands (rmsf_no_imaging.jpg), the rms > > fluctuation does not show any such sudden increase. > > I have attached the images of these plots. > > > > Why is this this strange behavior observed? > > How will I make sure which set of image center commands works better for > my > > system. > > > > Any suggestions would be very helpful. > > > > > > > > > > > > > > > > -- > > Thank you, > > > > With regards, > > B. Sangeetha > > Ph.D Scholar, > > Centre for Bioinformatics, > > Pondicherry University, > > Pondicherry, > > India > > > > _______________________________________________ > > AMBER mailing list > > AMBER.ambermd.org > > http://lists.ambermd.org/mailman/listinfo/amber > > > > > > -- > ------------------------- > Daniel R. Roe, PhD > Department of Medicinal Chemistry > University of Utah > 30 South 2000 East, Room 201 > Salt Lake City, UT 84112-5820 > http://home.chpc.utah.edu/~cheatham/ > (801) 587-9652 > (801) 585-9119 (Fax) > > _______________________________________________ > 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/amberReceived on Thu Dec 06 2012 - 04:30:02 PST