[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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--
========================================
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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