[gmx-users] so difficult problem

Justin A. Lemkul jalemkul at vt.edu
Sat Jan 15 15:40:42 CET 2011



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>> 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>> 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>> 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...
>>             >>
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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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> 
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-- 
========================================

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

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