Dear justin I generated it by PRODRG server,and modifying Protein.top as it is in ENZYME/DRUG tutorial. Actually I don't know where is problem. Ok,I will modify my EM parameter to do a good energy minimization. Thanks in advance
On Sat, Jan 15, 2011 at 6:10 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > mohsen ramezanpour wrote: > >> I checked this one but it did not solve the problem. >> Actually I did in your way and I found the force is very high on one atom >> of my ligand,C12. >> I checked it's structure with pymol,it 's situation was normal. >> can I change it's coordinate a few? >> I think it can make force less. >> please let me know how can i do >> > > Making ad hoc changes to coordinates is a bad idea. What you might gain by > relaxing nonbonded forces you might strain within the molecule (bonded > interactions). Proper energy minimization should resolve any high forces. > > What is your ligand? How did you generate its topology? Poor parameters > can also give bad contacts and forces. > > -Justin > > thanks in advance >> >> >> On Wed, Jan 12, 2011 at 3:22 PM, mohsen ramezanpour < >> ramezanpour.moh...@gmail.com <mailto:ramezanpour.moh...@gmail.com>> >> wrote: >> >> >> >> >> On Wed, Jan 12, 2011 at 2:59 PM, Mark Abraham >> <mark.abra...@anu.edu.au <mailto:mark.abra...@anu.edu.au>> wrote: >> >> On 12/01/2011 9:37 PM, mohsen ramezanpour wrote: >> >>> Dear Dr,Tsjerk >>> I want to estimate protein-drug binding free energy. >>> I am using umbrella sampling for this mean. >>> my drug is inside of a hole in protein. then I have to rotate >>> my system to can fit the pulling line along one box axis. >>> besides I have to pull drug not at direction which connect COM >>> of protein and drug,but it is better to pull it along line >>> which connects drug to >>> a residue inside of hole. >>> >> >> I would >> >> 1) take my starting bound configuration, >> 2) strip away anything except the protein complex, >> 3) delete the box information, >> 4) rotate the complex with editconf until I was happy with its >> orientation, >> 5) then generate a suitable box around that orientation, >> 6) do EM >> 7) solvate and neutralize >> 8) do EM >> 9) etc. >> >> Mark >> Dear Mark >> >> thanks for your reply >> I will check this ways too. >> >> >> >>> I rotated box with editconf ,solvated system with >>> genbox,neutralized with genion, >>> now I want to generate NPT and then generating configuration >>> as umbrella sampling tutorial. >>> >>> >>> >>> On Wed, Jan 12, 2011 at 1:53 PM, Tsjerk Wassenaar >>> <tsje...@gmail.com <mailto:tsje...@gmail.com>> wrote: >>> >>> Hi Mohsen, >>> >>> You're doing something terribly wrong. But why you want to >>> do what you >>> attempt eludes me. Maybe it helps if you give an >>> explanation of what >>> you want, in stead of what doesn't work. In addition, give >>> the set of >>> commands that bring you up to this point, and not only the >>> output of >>> mdrun. That way we can probably see where you go astray. >>> >>> Cheers, >>> >>> Tsjerk >>> >>> >>> On Wed, Jan 12, 2011 at 10:55 AM, mohsen ramezanpour >>> <ramezanpour.moh...@gmail.com >>> <mailto:ramezanpour.moh...@gmail.com>> wrote: >>> > >>> > Dear Dr.Tsjerk >>> > >>> > Before doing md for generating NPT, I did an EM,the >>> result was: >>> > poteintial energy:-2.2611160*10^(6) >>> > Max F=4.8960352*10^(4) on atom 5289 >>> > Besides I had done EM before on the same system,I just >>> add solvent by genbox >>> > and Ions by genion. >>> > the above result is for Energy minimization after adding >>> ions by genion. >>> > >>> > I did what you said.but when I was generating NPT >>> equilibration >>> > I recieved this massage: >>> > >>> > >>> > Step 0, time 0 (ps) LINCS WARNING >>> > relative constraint deviation after LINCS: >>> > rms 8.387059, max 321.381958 (between atoms 5289 and 5290) >>> > bonds that rotated more than 30 degrees: >>> > atom 1 atom 2 angle previous, current, constraint length >>> > 5293 5294 74.4 0.1137 12.9330 0.1090 >>> > 5291 5293 59.1 0.1422 32.1605 0.1390 >>> > 5291 5292 103.5 0.1096 9.8747 0.1090 >>> > 5289 5291 89.5 0.1383 39.2022 0.1390 >>> > 5289 5290 85.7 0.1410 43.8439 0.1360 >>> > 5289 5287 85.4 0.1426 44.0196 0.1390 >>> > 5287 5288 90.2 0.1091 1.5178 0.1090 >>> > 5285 5287 88.7 0.1391 1.9186 0.1390 >>> > 5285 5286 41.8 0.1092 0.1322 0.1090 >>> > 5284 5293 87.2 0.1429 21.7425 0.1390 >>> > 5284 5285 92.4 0.1393 2.0880 0.1390 >>> > 5277 5278 79.1 0.1532 0.5213 0.1530 >>> > 5276 5284 63.0 0.1394 1.8946 0.1390 >>> > 5276 5277 79.2 0.1534 0.7278 0.1530 >>> > 5276 5275 79.9 0.1432 0.6036 0.1430 >>> > 5274 5275 82.0 0.1431 0.3189 0.1430 >>> > 5276 5272 82.1 0.1393 0.6113 0.1390 >>> > 5272 5273 74.2 0.1333 0.2251 0.1330 >>> > 5272 5270 77.7 0.1332 0.2428 0.1330 >>> > 5270 5271 46.5 0.1091 0.1682 0.1090 >>> > 5268 5270 36.9 0.1391 0.1854 0.1390 >>> > 5273 5266 41.4 0.1334 0.1933 0.1330 >>> > Wrote pdb files with previous and current coordinates >>> > step 0Warning: 1-4 interaction between 5272 and 5293 at >>> distance 22.443 >>> > which is larger than the 1-4 table size 2.400 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 >>> > >>> > Please let me know what can I do. >>> > thanks in advance >>> > >>> > >>> > >>> > >>> > >>> > >>> > >>> > >>> > >>> > >>> > >>> > >>> > >>> > On Thu, Jan 6, 2011 at 11:20 PM, Tsjerk Wassenaar >>> <tsje...@gmail.com <mailto:tsje...@gmail.com>> wrote: >>> >> >>> >> Hi Mohsen, >>> >> >>> >> I think rotating a molecule with editconf will not >>> rotate the box. Then >>> >> again, if it did, it would result in a box violating >>> Gromacs requirements. >>> >> Either way, it's not going to work like that. Build a >>> new box after >>> >> rotation... And have a good look at what you're >>> actually trying now by >>> >> taking the rotated system and stack it a few times >>> using genconf -nbox 2 2 2 >>> >> >>> >> Cheers, >>> >> >>> >> Tsjerk >>> >> >>> >> On Jan 6, 2011 7:22 PM, "mohsen ramezanpour" >>> >> <ramezanpour.moh...@gmail.com >>> <mailto:ramezanpour.moh...@gmail.com>> wrote: >>> >> >>> >> Dear Amit >>> >> I entered these commands for rotating box: >>> >> editconf -f conf.gro -o output.pdb -rotate 0 >>> 0 25.4 >>> >> and then: >>> >> editconf -f output.pdb -o newbox.pdb -rotate 0 >>> 127.67548 0 >>> >> as a result my molecul is located out of box totally,of >>> course drug and >>> >> protein are bind to eachother yet. >>> >> thanks in advance for your attention and reply >>> >> >>> >> On Tue, Jan 4, 2011 at 1:25 PM, Amit Choubey >>> <kgp.a...@gmail.com <mailto:kgp.a...@gmail.com>> wrote: > >>> >> > Could you post the e... >>> >> >>> >> -- >>> >> gmx-users mailing list gmx-users@gromacs.org >>> <mailto:gmx-users@gromacs.org> >>> >>> >> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> >> Please search the archive at >>> >> http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists >>> >> >>> >> -- >>> >> gmx-users mailing list gmx-users@gromacs.org >>> <mailto:gmx-users@gromacs.org> >>> >>> >> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> >> Please search the archive at >>> >> http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists >>> > >>> > >>> > -- >>> > gmx-users mailing list gmx-users@gromacs.org >>> <mailto:gmx-users@gromacs.org> >>> >>> > http://lists.gromacs.org/mailman/listinfo/gmx-users >>> > Please search the archive at >>> > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists >>> > >>> >>> >>> >>> -- >>> Tsjerk A. Wassenaar, Ph.D. >>> >>> post-doctoral researcher >>> Molecular Dynamics Group >>> * Groningen Institute for Biomolecular Research and >>> Biotechnology >>> * Zernike Institute for Advanced Materials >>> University of Groningen >>> The Netherlands >>> -- >>> gmx-users mailing list gmx-users@gromacs.org >>> <mailto:gmx-users@gromacs.org> >>> >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists >>> >>> >>> >> >> -- >> gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists >> >> >> >> > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > 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/Support/Mailing_Lists/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/Support/Mailing_Lists >
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