Sory. My ligand is Citalopram(a drug) On Mon, Jan 17, 2011 at 1:35 PM, mohsen ramezanpour < ramezanpour.moh...@gmail.com> wrote:
> 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 >> > >
-- 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