[gmx-users] so difficult problem
mohsen ramezanpour
ramezanpour.mohsen at gmail.com
Mon Jan 17 11:05:13 CET 2011
Dear justin
I generated it by PRODRG server,and modifying Protein.top as it is in
ENZYME/DRUG tutorial.
Actually I don't know where is problem.
Ok,I will modify my EM parameter to do a good energy minimization.
Thanks in advance
On Sat, Jan 15, 2011 at 6:10 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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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