[gmx-users] so difficult problem
Justin A. Lemkul
jalemkul at vt.edu
Mon Jan 17 13:06:15 CET 2011
mohsen ramezanpour 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.
Back up and start over. PRODRG topologies (especially for a molecule as complex
as yours) are generally of very poor quality. Garbage in, garbage out. Even if
you manage to get the simulations running I wouldn't necessarily trust the
outcome. Please see the paper linked from:
http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips
You may want to re-think the force field entirely. Gromos96 parameter sets are
not particularly versatile when it comes to the types of functional groups that
can be described, making correct topology generation somewhat difficult for most
drug molecules.
-Justin
> Thanks in advance
>
> On Sat, Jan 15, 2011 at 6:10 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at 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.mohsen at gmail.com
> <mailto:ramezanpour.mohsen at gmail.com>
> <mailto:ramezanpour.mohsen at gmail.com
> <mailto:ramezanpour.mohsen at gmail.com>>> wrote:
>
>
>
>
> On Wed, Jan 12, 2011 at 2:59 PM, Mark Abraham
> <Mark.Abraham at anu.edu.au <mailto:Mark.Abraham at anu.edu.au>
> <mailto:Mark.Abraham at anu.edu.au
> <mailto:Mark.Abraham at 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
> <tsjerkw at gmail.com <mailto:tsjerkw at gmail.com>
> <mailto: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>
> <mailto: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>
> <mailto: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>
> <mailto: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>
> <mailto: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>
> <mailto: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>
> <mailto: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>
> <mailto: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>
> <mailto: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>
> <mailto: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>
> <mailto: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>
> <mailto: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>
> <mailto: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>
> <mailto: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>
> <mailto:gmx-users-request at gromacs.org
> <mailto:gmx-users-request at 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 <http://vt.edu> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> --
> 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
>
>
--
========================================
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
========================================
More information about the gromacs.org_gmx-users
mailing list