[gmx-users] so difficult problem

mohsen ramezanpour ramezanpour.mohsen at gmail.com
Wed Jan 12 11:37:49 CET 2011 

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 <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> 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>
> 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> 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>
> wrote: >
> >> > Could you post the e...
> >>
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>
> --
> 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
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