[gmx-users] so difficult problem

mohsen ramezanpour ramezanpour.mohsen at gmail.com
Wed Jan 12 12:50:15 CET 2011 

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 <tsjerkw at gmail.com> 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
> <ramezanpour.mohsen at gmail.com> 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 <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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>
> --
> 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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