[gmx-users] so difficult problem

mohsen ramezanpour ramezanpour.mohsen at gmail.com
Wed Jan 12 12:52:27 CET 2011


On Wed, Jan 12, 2011 at 2:59 PM, Mark Abraham <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>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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