An additional measure that may help is to use either STRIDE or DSSP on the intial and final structures and try to quantify how much the secondary structure has really changed.
-Micholas =================== Micholas Dean Smith, PhD. Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics ________________________________________ From: [email protected] <[email protected]> on behalf of Justin Lemkul <[email protected]> Sent: Tuesday, September 01, 2015 8:16 AM To: [email protected] Subject: Re: [gmx-users] structure changed after energy minimization On 9/1/15 8:14 AM, Smith, Micholas D. wrote: > Hi Sana Saeed, > > What force field are you using? Also are you sure the structure you are > starting with is stable to begin with? It is possible that the model you are > starting with is actually fairly far away from the minimum energy structure > in which case energy minimization may alter the structure (though i've never > seen a beta sheet changing into a coil-like form). > Worth noting that visualization software sometimes fails to render secondary structure correctly. Analyzing the hydrogen bonding and backbone dihedrals is definitive; whatever VMD/PyMOL/etc come up with is not. -Justin > -Micholas > > =================== > Micholas Dean Smith, PhD. > Post-doctoral Research Associate > University of Tennessee/Oak Ridge National Laboratory > Center for Molecular Biophysics > > ________________________________________ > From: [email protected] > <[email protected]> on behalf of Sana Saeed > <[email protected]> > Sent: Monday, August 31, 2015 10:30 PM > To: [email protected] > Subject: [gmx-users] structure changed after energy minimization > > hi gmx users,i want to simulate prion protein(beta-sheets structure; model in > modeller), but after minimization the structure totally changes into > elongated form.what am i missing? i am doing implicit solvent simulation. > this is the mdp file for minimization: title =cpp > = /lib/cpp ; prepocessor > of the current machinedefine = -DFLEXIBLE > ; -DPOSRES, -DPOSRES_IONS ;DFLEX_SPC; FLEXible SPC > and POSition REStraints > integrator = steep > ; steepest descent algorithmdt = 0.005 > ; time step in psnsteps = 5000 > ; number of steps > emtol = 100 > ; convergence criterionemstep = 0.05 > ; intial step sizeconstraints = > noneconstraint-algorithm = lincsunconstrained-start = no > ; Do not constrain the start > configuration;shake_tol = 0.0001nstlist = 1 > ; step frequency for updating > neighbour listns_type = simple > ; grid ; method for nighbour searching (?)nstxout > = 100 ; frequency for > writing coords to outputnstvout = 100 > ; frequency for writing velocities to outputnstfout > = 0 ; frequency for writing forces to outputnstlog > = > 100 ; frequency for writing energies to log filenstenergy = > 100 ; frequency for writing energies to energy filenstxtcout = 0 > ; frequency for writing coords to xtc trajxtc_grps = system ; > group(s) whose coords are to be written in xtc trajenergygrps = > system ; group(s) whose energy is to be written in energy filepbc > = xyz ; use pbcrlist = 1.0 ; cutoff (nm)coulombtype > = cutoff ; truncation for minimisation, with large cutoffrcoulomb > = 1.0vdwtype = cut-off ; truncation for minimisation, > with large cutoffrvdw = 1.0nstcomm = 0 ; number > of steps for centre of mass motion removal (in vacuo only!)Tcoupl > = noPcoupl = nogen_vel = no Free energy control > stufffree_energy = yesinit_lambda = 0.0delta_lambda > = 0sc_alpha =0.5sc-power > =1.0sc-sigma = 0.3 > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to [email protected]. > -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 [email protected] | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected]. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
