[gmx-users] so difficult problem

mohsen ramezanpour ramezanpour.mohsen at gmail.com
Sat Jan 15 15:36:19 CET 2011 

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
thanks in advance

On Wed, Jan 12, 2011 at 3:22 PM, mohsen ramezanpour <
ramezanpour.mohsen at gmail.com> wrote:

>
>
>
> 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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