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 thanks in advance
On Wed, Jan 12, 2011 at 3:22 PM, mohsen ramezanpour < [email protected]> wrote: > > > > On Wed, Jan 12, 2011 at 2:59 PM, Mark Abraham <[email protected]>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 <[email protected]>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 >>> <[email protected]> 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 <[email protected]> >>> 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" >>> >> <[email protected]> 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 <[email protected]> >>> wrote: > >>> >> > Could you post the e... >>> >> >>> >> -- >>> >> gmx-users mailing list [email protected] >>> >> 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 [email protected]. >>> >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >> >>> >> -- >>> >> gmx-users mailing list [email protected] >>> >> 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 [email protected]. >>> >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> > >>> > >>> > -- >>> > gmx-users mailing list [email protected] >>> > 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 [email protected]. >>> > 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 [email protected] >>> 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 [email protected]. >>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >> >> >> >> -- >> gmx-users mailing list [email protected] >> 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 [email protected]. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > >
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