[gmx-users] so difficult problem
mohsen ramezanpour
ramezanpour.mohsen at gmail.com
Mon Jan 17 11:06:53 CET 2011
Sory.
My ligand is Citalopram(a drug)
On Mon, Jan 17, 2011 at 1:35 PM, mohsen ramezanpour <
ramezanpour.mohsen at gmail.com> wrote:
> 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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>> --
>> ========================================
>>
>> 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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>
>
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