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
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 <[email protected]
<mailto:[email protected]>> 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
<[email protected]
<mailto:[email protected]>> 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
<[email protected] <mailto:[email protected]>> 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"
>> <[email protected]
<mailto:[email protected]>> 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
<[email protected] <mailto:[email protected]>> 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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