Dear David, Thanks for the reply, guess i will do some literature survey and see if i can find some validated urea parameters.
karan On Mon, Sep 21, 2009 at 8:51 PM, David van der Spoel <[email protected]>wrote: > karan syal wrote: > >> Dear Justin, >> >> Thanks for the reply! >> >> I will surely try minimize the protein in Vacuum and then try adding Urea >> again. >> >> Just that i was wondering how will that effect my artifact bonds which are >> between Urea and Water, and not at all between any Protein atom and >> Urea/Sol?? As i mentioned earlier, these bonds are formed only after >> minimization, they are not present before adding 10M urea+water box (No such >> bonds in its individual 10M urea+water .gro either ) to protein, they are >> neither there in the before minimized protein+10M urea+water system. >> >> Don't use the Urea topology that is in the gromacs distribution. It is > not based on any force field known to man. > >> >> Thanks again, >> >> cherrz >> karan >> >> >> On Mon, Sep 21, 2009 at 4:11 PM, Justin A. Lemkul <[email protected]<mailto: >> [email protected]>> wrote: >> >> >> >> karan syal wrote: >> >> Dear Gromacs users, >> >> I am trying to run a urea+protein simulation and encountering a >> few problems at various stages. >> >> I have taken an equilibrated 10M urea box of size >> 2.84nmx2.84nmx2.84nm (I started with 3x3x3 containing 160 urea + >> 398 SOL, ran NPT @ 1 bar and 300K) >> >> I am using this equilibrated box to add to a globular protein of >> about 250 residues using following commands : >> >> >> editconf -f P48.gro -o P48_box.gro -c -d 0.6 -bt dodecahedron >> (Giving me a dodecahedron with Vol = 407.98nm^3, so for this >> volume, for 10M urea the number of urea above box should add is >> 2448.) >> >> genbox -cp P48_box.gro -cs 10Murea.gro -o P48_10MUrea.gro >> (*This adds 2064 Urea only, shouldnt it be adding 2448 urea >> molecules, corresponding to 10M urea box i have solvated with??)* >> >> >> No, it shouldn't. The protein occupies space within that volume, as >> well. >> >> >> >> When i try to minimize this using the following em.mdp >> >> >> cpp = /usr/bin/cpp >> constraints = none >> integrator = steep >> nsteps = 5000 >> coulombtype = PME >> pme_order = 4 >> nstlist = 5 >> ns_type = grid >> rlist = 1.0 >> rcoulomb = 1.0 >> rvdw = 1.0 >> Tcoupl = no >> Pcoupl = no >> fourierspacing = 0.12 >> fourier_nx = 0 >> fourier_ny = 0 >> fourier_nz = 0 >> ; Energy minimizing stuff >> ; >> emtol = 100 >> emstep = 0.01 >> >> >> *It gives me the following output* >> >> >> Steepest Descents: >> Tolerance (Fmax) = 1.00000e+02 >> Number of steps = 5000 >> Warning: 1-4 interaction between 2796 and 2801 at distance 2.727 >> which is larger than the 1-4 table size 2.000 nm >> These are ignored for the rest of the simulation >> This usually means your system is exploding, >> if not, you should increase table-extension in your mdp file >> or with user tables increase the table size >> >> t = 0.015 ps: Water molecule starting at atom 34477 can not be >> settled. >> Check for bad contacts and/or reduce the timestep. >> Wrote pdb files with previous and current coordinates >> >> Stepsize too small, or no change in energy. >> Converged to machine precision, >> but not to the requested precision Fmax < 100 >> >> Double precision normally gives you higher accuracy. >> You might need to increase your constraint accuracy, or turn >> off constraints alltogether (set constraints = none in mdp file) >> >> writing lowest energy coordinates. >> >> Steepest Descents converged to machine precision in 34 steps, >> but did not reach the requested Fmax < 100. >> Potential Energy = -1.3092671e+22 >> Maximum force = inf on atom 12598 >> Norm of force = inf >> >> gcq#160: "The Microsecond is Within Reach" (P.J. Van Maaren) >> >> >> >> /When i look at the file in VMD, the protein is completely out >> of the box + There are unusual bonds between a lot of UREA and >> SOL molecules/. ( The unusual bonds are artifcats after >> minimization which are not there when i initially look at my >> P48_10Mrea.gro, that is the gro generated after genbox wth -cs >> as 10M urea) >> >> >> "Out of the box" doesn't exist for a periodic system. The "bonds" >> you see are also *not* generated by Gromacs, but are also just an >> artefact of visualization. Bonds are not created or broken in >> molecular mechanics. >> >> >> I tried constraining hbonds as well in em.mdp bit to no effect. >> >> >> I used the above em.gro to run a production run, with following >> pr.mdp >> >> >> Don't, it's a waste of time. Never just plow ahead when something >> isn't working. There is something unreasonable about the starting >> structure. Try minimizing the protein in vacuo first, then add your >> urea and try EM again. >> >> -Justin >> >> -- ======================================== >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> _______________________________________________ >> gmx-users mailing list [email protected] >> <mailto:[email protected]> >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to [email protected] >> <mailto:[email protected]>. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> gmx-users mailing list [email protected] >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php >> > > > -- > David van der Spoel, Ph.D., Professor of Biology > Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. > [email protected] [email protected] http://folding.bmc.uu.se > > _______________________________________________ > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php >
_______________________________________________ gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
