[gmx-users] so difficult problem
Mark Abraham
Mark.Abraham at anu.edu.au
Wed Jan 12 12:29:36 CET 2011
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
>
> 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 <tsjerkw at gmail.com
> <mailto:tsjerkw at 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.mohsen at gmail.com
> <mailto:ramezanpour.mohsen at 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
> <tsjerkw at gmail.com <mailto:tsjerkw at 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.mohsen at gmail.com
> <mailto:ramezanpour.mohsen at 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.amit at gmail.com <mailto:kgp.amit at gmail.com>> wrote: >
> >> > Could you post the e...
> >>
> >> --
> >> gmx-users mailing list gmx-users at gromacs.org
> <mailto:gmx-users at 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-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>.
> >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> >> --
> >> gmx-users mailing list gmx-users at gromacs.org
> <mailto:gmx-users at 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-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>.
> >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> >
> > --
> > gmx-users mailing list gmx-users at gromacs.org
> <mailto:gmx-users at 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-request at gromacs.org
> <mailto:gmx-users-request at 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 at gromacs.org
> <mailto:gmx-users at 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-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110112/536d0aa0/attachment.html>
More information about the gromacs.org_gmx-users
mailing list