Respected Sir, Greetings from Pawan. I have edited the lipid.itp file to add just one line extra " H atom from the opls_force_filed.itp " at the end of lipid interactions data and that works fine. I have done this after seeing the archives. It was given either I should change the file for sigma and epsilon values or else just add this line. I think I have done it correctly. If not please correct me. I have removed the position restraints after the inflategro procedure. After that I did energy minimization using define = -DFLEXIBLE. I will change the temperature as per your suggestion. I thought before solvating if I do position restraint mdrun the lipids will compact more surrounding the protein. Thats the step when I got Lincs warnings and segmentation fault. Then I tried solvating the system using genbox step and spc216.gro as the solvent. But before doing the solvation step I copied the vdwradii.dat file into the working directory and increased the value for carbon to 0.5. But the result of this was " Segmentation fault " again. Can you please tell me why I get the " Segmentation fault " here in this step. The command used was : genbox -cp comp_em27.pdb -cs spc216.gro -o box.pdb -p topol.top
Thanking you, Yours sincerely, Pawan On Tue, Mar 31, 2009 at 4:20 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Justin A. Lemkul wrote: > >> >> >> Pawan Kumar wrote: >> >>> Respected Sir, >>> >>> Greetings from Pawan. >>> I have used force constants of 100000 in position restraint .itp files >>> for proteins as suggested in Dr. Tieleman' s webisite for Inflategro. >>> The mdp files are : >>> >> >> The .mdp files look reasonable enough, although I don't know why you are >> applying position restraints during EM. If it is for InflateGRO, that is >> fine, but once the system is assembled, you should remove the position >> restraints from the protein to minimize the system more. >> >> And are you sure you want 300K? DPPC will be in a gel phase at that >> temperature. If you want a more realistic fluid-phase model, you'll have to >> go above 315K (323K is common). >> >> > One thing I just noticed. You don't have solvent in your > position-restrained run? That could be a big problem if the lipid > headgroups are strongly repelled from one another. Add solvent before doing > anything other than EM. > > -Justin > > > *Topology file :* >>> ; Include forcefield parameters >>> #include "ffoplsaa.itp" >>> #include "lipid.itp" >>> #include "dppc.itp" >>> >>> >> This section should not work, as written. Have you modified lipid.itp >> according to Chris Neale's half-epsilon double-pairlist method? If not, >> what you've done makes no sense. The Berger lipid parameters distributed >> through Tieleman's site are designed for use with the Gromos force fields. >> They can be modified (search in the archives), but that can also be a >> source of error. Users who have made mistakes in the conversion have seen >> their systems explode. >> >> -Justin >> >> ; Include chain topologies >>> #include "topol_A.itp" >>> #include "topol_B.itp" >>> #include "topol_C.itp" >>> >>> ;#ifdef POSRES >>> ;#include "lipid_posre.itp" >>> ;#endif >>> >>> ; Include water topology >>> #ifdef FLEX_SPC >>> #include "flexspc.itp" >>> #else >>> #include "spc.itp" >>> #endif >>> >>> #ifdef POSRES_WATER >>> ; Position restraint for each water oxygen >>> [ position_restraints ] >>> ; i funct fcx fcy fcz >>> 1 1 1000 1000 1000 >>> #endif >>> >>> ; Include generic topology for ions >>> #include "ions.itp" >>> >>> [ system ] >>> ; Name >>> PROTEIN IN DPPC BILAYER >>> >>> [ molecules ] >>> ; Compound #mols >>> Protein_A 1 >>> Protein_B 1 >>> Protein_C 1 >>> DPPC 926 >>> ;SOL 23552 >>> >>> Please help with some suggestions. >>> >>> Thanking you, >>> >>> Yours sincerely, >>> Pawan >>> >>> On Mon, Mar 30, 2009 at 6:22 PM, Justin A. Lemkul <jalem...@vt.edu<mailto: >>> jalem...@vt.edu>> wrote: >>> >>> Pawan Kumar wrote: >>> >>> Respected Sir, >>> >>> Greetings from Pawan. >>> I did the Inflategro procedure for the POPC bilayer generated >>> using genconf. >>> It took around 26 compressions for coming near the initial area >>> (just above it). >>> The minimization were all converged to Fmax < 1350. >>> If I decrease the Fmax less than this I am getting machine >>> precision. >>> But when I proceeded with the final compressed structure for pr >>> mdrun it gave lincs warnings and ended with segmentation fault. >>> As an alternative to this bilayer I used the DPPC bilayer >>> (pre-equilibrated) which is given in GMX-Benchmark distribution. >>> I carried out the same steps of Inflategro. I used the cutoff of >>> 14 A in the inflation and compression step also. >>> In this case the the Steepest Descents converged to Fmax < 1000 >>> in all the steps. The maximum force war never above 850. >>> But when I did position restraint mdrun with the last compressed >>> file I got Lincs warnings and Segementation fault after few >>> steps (30 - 40 steps). >>> Can you please help how to proceed ? >>> >>> >>> If the minimization procedure is adequately finishing, then the >>> problem comes from something you are doing. If you post your .mdp >>> file, we may be able to see if there are any obvious mistakes. >>> >>> -Justin >>> >>> Thanking you, >>> >>> Yours sincerely, >>> Pawan >>> >>> >>> Justin A. Lemkul >>> Graduate Research Assistant >>> 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 gmx-users@gromacs.org >>> <mailto:gmx-users@gromacs.org> >>> http://www.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 gmx-users-requ...@gromacs.org >>> <mailto:gmx-users-requ...@gromacs.org>. >>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>> >>> >>> >> > -- > ======================================== > > Justin A. Lemkul > Graduate Research Assistant > ICTAS Doctoral Scholar > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.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 gmx-users-requ...@gromacs.org. > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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