Dear MARK and Tsjerk Thanks for your advises..... Considering to my input and out put I should say that I mention to the chain and in pdb file chain A and chain B are separate.... also I cheked toplogy and the structure after pdb2gmx...the atoms in topology are reasonable and gro file does not have any problem...
and also I told you that the structure also have problem with amber forcefield...it seems that the structure has problem with All ATom forcefield........ The energy of structure after minimization by gromacs is : Step 1427, Epot=-4.410279e+04, Fnorm=2.888e+01, Fmax=8.733e+02 (atom 42) Step 1428, Epot=-4.410310e+04, Fnorm=7.615e+00, Fmax=8.470e+01 (atom 2718) writing lowest energy coordinates. Polak-Ribiere Conjugate Gradients converged to Fmax < 100 in 1428 steps Potential Energy = -4.4103102e+04 Maximum force = 8.4704674e+01 on atom 2718 Norm of force = 7.6154613e+00 yours morteza > Send gmx-users mailing list submissions to > gmx-users@gromacs.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.gromacs.org/mailman/listinfo/gmx-users > or, via email, send a message with subject or body 'help' to > gmx-users-requ...@gromacs.org > > You can reach the person managing the list at > gmx-users-ow...@gromacs.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gmx-users digest..." > > > Today's Topics: > > 1. minimization (Morteza Khabiri) > 2. Re: minimization (Mark Abraham) > 3. Re: Fatal Equilibration Errors (Bruce D. Ray) > 4. Re: minimization (Tsjerk Wassenaar) > 5. solvation (Jamie Seyed) > 6. Re: solvation (Justin A. Lemkul) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 13 Aug 2009 11:30:03 +0200 (CEST) > From: "Morteza Khabiri" <khab...@greentech.cz> > Subject: [gmx-users] minimization > To: gmx-users@gromacs.org > Message-ID: > <25565.160.217.215.124.1250155803.squir...@www.greentech.cz> > Content-Type: text/plain;charset=iso-8859-2 > > Dear Tsjerk > > Thanks for your suggestion...actually It is a crystal structure...the > problem happen when I want to minimize the structure in vacuum....the box > size is enough...but the problem is that the minimization is fine with > gromacs forcefield but it is not ok with OPLSAA forcefiled....I tried to > minimized structure well by gromacs force file and the I took the > minimized structure from gromacs forcefield and then I tried it in OPLSAA > and the problem was the same as before... I also cut my structure to some > pieces ( which I think that it is not reasonable) but I did it but still > it is not working....and the interesting point is that the protein is > working by gromacs forcefield well without any problem but when I want to > use the OPLSAA force field the problem > start and I could not minimized my system..I also try the AMBER forcefield > but the AMBER also didi not work and the result was the same as OPLSAA, > system was exploding.......when I want use all atom the problem appear and > I really don't know how to manage it..I already tried different coulomb > type algorythm and also different integrator,, different time > step..different emtol........but none of them working....... > > I would be happy if somebody could suggest me how could I manage it with > all atom forcefield... > > thanks > > > > > > > ------------------------------ > > Message: 2 > Date: Thu, 13 Aug 2009 20:56:22 +1000 > From: Mark Abraham <mark.abra...@anu.edu.au> > Subject: Re: [gmx-users] minimization > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4a83f156.2020...@anu.edu.au> > Content-Type: text/plain; charset=ISO-8859-2; format=flowed > > Morteza Khabiri wrote: >> Dear Tsjerk >> >> Thanks for your suggestion...actually It is a crystal structure...the >> problem happen when I want to minimize the structure in vacuum....the >> box >> size is enough...but the problem is that the minimization is fine with >> gromacs forcefield but it is not ok with OPLSAA forcefiled.... > > That seems intrinsically improbable, unless the oplsaa .hdb and .tdb > files are not coping with the structure (somehow) and generating a > broken starting configuration and/or topology. What was the final PE and > maximum force from the gromacs forcefield EM? I suggest you look > carefully at the post-pdb2gmx oplsaa structure for steric clashes, > unsatisified valences, etc., and then look at the progress of the > corresponding minimization. You should see evidence of whatever is wrong. > > Mark > >> I tried to >> minimized structure well by gromacs force file and the I took the >> minimized structure from gromacs forcefield and then I tried it in >> OPLSAA >> and the problem was the same as before... I also cut my structure to >> some >> pieces ( which I think that it is not reasonable) but I did it but still >> it is not working....and the interesting point is that the protein is >> working by gromacs forcefield well without any problem but when I want >> to >> use the OPLSAA force field the problem >> start and I could not minimized my system..I also try the AMBER >> forcefield >> but the AMBER also didi not work and the result was the same as OPLSAA, >> system was exploding.......when I want use all atom the problem appear >> and >> I really don't know how to manage it..I already tried different coulomb >> type algorythm and also different integrator,, different time >> step..different emtol........but none of them working....... >> >> I would be happy if somebody could suggest me how could I manage it with >> all atom forcefield... >> >> thanks >> >> >> >> >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> 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 gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > > ------------------------------ > > Message: 3 > Date: Thu, 13 Aug 2009 04:42:57 -0700 (PDT) > From: "Bruce D. Ray" <bruced...@yahoo.com> > Subject: Re: [gmx-users] Fatal Equilibration Errors > To: gmx-users@gromacs.org > Message-ID: <989464.1354...@web35801.mail.mud.yahoo.com> > Content-Type: text/plain; charset="us-ascii" > > On Wednesday, August 12, 2009 at 8:47:33 PM, Nancy <nancy5vi...@gmail.com> > wrote: > >> In an earlier message, it was stated that topolbuild generated > topologies with Gromos 53a6 >> and OPLS-AA force fields. I am using > topolbuild (version 1.2.2), and the only files in the >> "dat/gromacs" > directory are for the force fields: 43a1, 43a2, 43b1, 45a3, 53a5, and > 53a6. >> How is the OPLS-AA force field used? > > First, I need to thank you in particular. First, while testing your > molecules, I discovered a > case in the as yet unreleased topolbuild 1.3 in which my dihedral > selection method failed > to select the dihedral choice with the maximum number of heavy atoms with > OPLS-AA as > the force field. Second, also because of this, I discovered what one > downloads as a "Sybyl > 2" structure from one source of small molecule structures and how to edit > it so that it meets > the syntax standards for a true mol2 file. Thank you very much for this > assistance. > > In the earlier message, I stated that topolbuild 1.2.1 ( and 1.2.2) > generates topologies for > amber, gaff, glycam, 43a1, 43a2, 43b1, 45a3, 53a5, and > 53a6. I stated that the as yet > unreleased topolbuild 1.3 will include OPLS-AA. The version of topolbuild > you have, > is 1.2.2. Would you like to beta test topolbuild 1.3? > > > Sincerely, > > -- > Bruce D. Ray, Ph.D. > Associate Scientist > IUPUI > Physics Dept. > 402 N. Blackford St. > Indianapolis, IN 46202-3273 > > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20090813/e945f426/attachment-0001.html > > ------------------------------ > > Message: 4 > Date: Thu, 13 Aug 2009 15:46:33 +0200 > From: Tsjerk Wassenaar <tsje...@gmail.com> > Subject: Re: [gmx-users] minimization > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: > <8ff898150908130646j2e1f415ew41dc8c0092dc...@mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Hmm, was the OPLSAA run following the GMX one on the dimer or also > performed on the monomers? If you feed a multimeric protein without > chain identifiers (like in a .gro file) to pdb2gmx, it will bind the > different chains together. That would be a good cause for a crash. So > I'd say check that first, and check the output from pdb2gmx > thoroughly. Also see if you end up with each chain in its own .itp > file. > > Cheers, > > Tsjerk > > 2009/8/13 Mark Abraham <mark.abra...@anu.edu.au>: >> Morteza Khabiri wrote: >>> >>> Dear Tsjerk >>> >>> Thanks for your suggestion...actually It is a crystal structure...the >>> problem happen when I want to minimize the structure in vacuum....the >>> box >>> size is enough...but the problem is that the minimization is fine with >>> gromacs forcefield but it is not ok with OPLSAA forcefiled.... >> >> That seems intrinsically improbable, unless the oplsaa .hdb and .tdb >> files >> are not coping with the structure (somehow) and generating a broken >> starting >> configuration and/or topology. What was the final PE and maximum force >> from >> the gromacs forcefield EM? I suggest you look carefully at the >> post-pdb2gmx >> oplsaa structure for steric clashes, unsatisified valences, etc., and >> then >> look at the progress of the corresponding minimization. You should see >> evidence of whatever is wrong. >> >> Mark >> >>> I tried to >>> minimized structure well by gromacs force file and the I took the >>> minimized structure from gromacs forcefield and then I tried it in >>> OPLSAA >>> and the problem was the same as before... I also cut my structure to >>> some >>> pieces ( which I think that it is not reasonable) but I did it but >>> still >>> it is not working....and the interesting point is that the protein is >>> working by gromacs forcefield well without any problem but when I want >>> to >>> use the OPLSAA force field the problem >>> start and I could not minimized my system..I also try the AMBER >>> forcefield >>> but the AMBER also didi not work and the result was the same as OPLSAA, >>> system was exploding.......when I want use all atom the problem appear >>> and >>> I really don't know how to manage it..I already tried different coulomb >>> type algorythm and also different integrator,, different time >>> step..different emtol........but none of them working....... >>> >>> I would be happy if somebody could suggest me how could I manage it >>> with >>> all atom forcefield... >>> >>> thanks >>> >>> >>> >>> >>> _______________________________________________ >>> gmx-users mailing list gmx-us...@gromacs.org >>> 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 gmx-users-requ...@gromacs.org. >>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>> >> _______________________________________________ >> gmx-users mailing list gmx-us...@gromacs.org >> 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 gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > > > -- > Tsjerk A. Wassenaar, Ph.D. > Junior UD (post-doc) > Biomolecular NMR, Bijvoet Center > Utrecht University > Padualaan 8 > 3584 CH Utrecht > The Netherlands > P: +31-30-2539931 > F: +31-30-2537623 > > > ------------------------------ > > Message: 5 > Date: Thu, 13 Aug 2009 11:37:00 -0400 > From: Jamie Seyed <jamie.se...@gmail.com> > Subject: [gmx-users] solvation > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: > <a9e5cd7b0908130837q38477e2djae8264d1ab896...@mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Dear all, > I want to know how can I use genbox to fill inside of the pore as well as > a > layer outside. From the "man genbox" page I try to use -shell with a > negative value (?) but it put waters far from the outside of the pore and > I > think it does not care about the sign. It seems strange to me because when > I > had 10 10 10 in the last line of my f.gro, by a shell 0.5 or 0.2, I got a > layer of few molecule around the pore, but when I change it to 1. 1. 1., > the > water molecules generated far away. I appreciate if someone tell me (1) > how > I can add water inside the pore and (2) why changing the box size will > give > a opposite result. Please advise..Thanks in advance/Jamie > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20090813/4a33fdec/attachment-0001.html > > ------------------------------ > > Message: 6 > Date: Thu, 13 Aug 2009 11:42:36 -0400 > From: "Justin A. Lemkul" <jalem...@vt.edu> > Subject: Re: [gmx-users] solvation > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4a84346c....@vt.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > Jamie Seyed wrote: >> Dear all, >> I want to know how can I use genbox to fill inside of the pore as well >> as a layer outside. From the "man genbox" page I try to use -shell with >> a negative value (?) but it put waters far from the outside of the pore >> and I think it does not care about the sign. It seems strange to me >> because when I had 10 10 10 in the last line of my f.gro, by a shell 0.5 >> or 0.2, I got a layer of few molecule around the pore, but when I change >> it to 1. 1. 1., the water molecules generated far away. I appreciate if >> someone tell me (1) how I can add water inside the pore and (2) why > > (1) The -vdwd option may help, or even -ci -nmol. If you have a pore, > wouldn't > water diffuse in over time anyway during equilibration (assuming an > otherwise > correct setup and realistic physical model)? > > (2) If you haven't re-positioned your system within the box, it probably > doesn't > make any sense. The Gromacs convention is to place the corner of the box > at the > coordinate origin, and everything else is relative to that. Is a 1-nm > cubic box > large enough to encompass your system? If not, genbox is doing what it's > told - > filling a 1-nm box near the origin, and leaving everything else out. > > -Justin > >> changing the box size will give a opposite result. Please advise..Thanks >> in advance/Jamie >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> 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 gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > 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://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > > End of gmx-users Digest, Vol 64, Issue 93 > ***************************************** > _______________________________________________ gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? 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