Hi Mohsen, You started off with a pdb file or so. What commands (full command lines) did you issue to get to the point where you are?...
Tsjerk On Wed, Jan 12, 2011 at 11:37 AM, mohsen ramezanpour <[email protected]> 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 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 > -- 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
