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
