Respected Sir, Greetings from Pawan. Thanks for all your kind help and suggestions. I will work on this and ask you if I have further doubts. Is it fine if I use the perl code given in wiki.gromacs.org/membrane-simulations for solvation after the genbox step to remove extra waters from the hydrophobic part of the bilayer ?
Thanking you, Yours sincerely, Pawan On Tue, Mar 31, 2009 at 5:31 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Pawan Kumar wrote: > >> Respected Sir, >> >> Greetings from Pawan. >> Thanks for all your suggestions. >> Is it possible to use the lipid.itp file from Tieleman sir's website in >> combination with GROMOS 96 force field without any modification ? >> > > If you want to use lipid.itp without any modification, you are restricted > to the ffgmx (deprecated!) force field. For Gromos96-lipid.itp combination, > simply remove the ";; parameters for lipid-GROMOS interactions," as these > nonbonded combinations are for ffgmx only. Otherwise, the nonbonded > interactions (which now have consistent combination rules) should be > generated correctly. > > Is it fine if I use the Gromos/Berger force field combination for the >> system I am using ? >> > > That is a decision you will have to make based on a thorough examination of > the literature, and the benefits and criticisms of these particular force > field parameters. > > I am sorry to ask this but can you please help me with some information >> how to modify the lipid.itp file ? >> > > That depends entirely upon what you want to do. If you want Gromos/Berger, > I've already told you. If you want OPLS/modified Berger, search the > archives for Chris Neale's posts on that topic. > > -Justin > > I will edit vdwradii.dat file as per your suggestion. >> >> >> Thanking you, >> >> Yours sincerely, >> Pawan >> >> On Tue, Mar 31, 2009 at 4:53 PM, Justin A. Lemkul <jalem...@vt.edu<mailto: >> jalem...@vt.edu>> wrote: >> >> >> >> Pawan Kumar wrote: >> >> 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. >> >> >> No, that is incorrect. You need to add the additional atom type as >> well as convert C6/C12 to sigma/epsilon. Otherwise, the calculated >> nonbonded interactions are meaningless. Read instructions carefully! >> >> Force fields have to be internally self-consistent, so using the >> parameters from OPLS with Berger lipids will give spurious results. >> The only proper combinations are Gromos/Berger or OPLS/converted >> Berger. >> >> >> 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. >> >> >> No, your system will probably explode due to unsatisfied charge >> interactions and hydrogen bonds. There is a substantial dipole in >> each lipid headgroup that can repel the lipids away from each other >> if it is not shielded. >> >> >> 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 >> >> >> Using a 0.5-nm radius for carbon will cause problems of excess >> memory consumption, or otherwise breaks the calculation. Use >> something more along the lines of 0.35 or 0.375, and manually delete >> out any stray waters in the hydrophobic core. >> >> -Justin >> >> >> Thanking you, >> >> Yours sincerely, >> Pawan >> >> On Tue, Mar 31, 2009 at 4:20 PM, Justin A. Lemkul >> <jalem...@vt.edu <mailto:jalem...@vt.edu> >> <mailto:jalem...@vt.edu <mailto: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> >> <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>> >> <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu> >> <mailto: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> >> <http://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> >> <mailto:gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org>> >> <mailto:gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> <mailto: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> >> <mailto:gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>> >> <mailto:gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org> >> <mailto: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 <http://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> >> <mailto: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/searchbefore >> 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> >> <mailto: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 <http://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 >> > > -- > ======================================== > > 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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