Dear yes,I did my work with pdb files. these are my commands after generating complex.gro and complex.top(according to Enzyme/Drug tutorial) editconf -f complex.gro -o box.pdb -d 1.0 -angles 90 90 90 ;for generating a typical rectangular box editconf -f box.pdb -o first-box -vec 5 5 20 -translate 0 0 4 ;to make a rectangular box with wanted length editconf -f first-box -o second-box -rotate 0 0 6 ;to rotate box around it's z axis editconf -f second-box -o third-box -rotate 0 127 0 ;to rotate box around it's y axis genbox -cp third-box -cs spc216 -p complex.top -o solvent.pdb ;to make solvate grompp -f ion.mdp -c solvent.pdb -o solvent-ion.tpr -p complex.top genion -s solvent-ion.tpr -o solvent-ion.pdb -p complex.top -neutral -nn 3 grompp -f minim.mdp -c solvent-ion.pdb -o solvent-ion-EM.tpr -p complex.top mdrun -v -deffnm solvent-ion-EM grompp -f npt.mdp -c solvate-ion-EM.pdb -o NPT.tpr mdrun -v -deffnm NPT
On Wed, Jan 12, 2011 at 2:17 PM, Tsjerk Wassenaar <[email protected]> wrote: > 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 >
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