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On 12/01/2011 9:37 PM, mohsen ramezanpour wrote:
<blockquote
cite="mid:AANLkTinGAcmUQ2yZ+CMEjLBjwjEH-BbT_-aYkA5a_gp3@mail.gmail.com"
type="cite">Dear Dr,Tsjerk<br>
I want to estimate protein-drug binding free energy.<br>
I am using umbrella sampling for this mean.<br>
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.<br>
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 <br>
a residue inside of hole.<br>
</blockquote>
<br>
I would <br>
<br>
1) take my starting bound configuration, <br>
2) strip away anything except the protein complex,<br>
3) delete the box information,<br>
4) rotate the complex with editconf until I was happy with its
orientation,<br>
5) then generate a suitable box around that orientation,<br>
6) do EM<br>
7) solvate and neutralize<br>
8) do EM<br>
9) etc.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:AANLkTinGAcmUQ2yZ+CMEjLBjwjEH-BbT_-aYkA5a_gp3@mail.gmail.com"
type="cite"><br>
I rotated box with editconf ,solvated system with
genbox,neutralized with genion,<br>
now I want to generate NPT and then generating configuration as
umbrella sampling tutorial.<br>
<br>
<br>
<br>
<div class="gmail_quote">On Wed, Jan 12, 2011 at 1:53 PM, Tsjerk
Wassenaar <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid
rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left:
1ex;">Hi Mohsen,<br>
<br>
You're doing something terribly wrong. But why you want to do
what you<br>
attempt eludes me. Maybe it helps if you give an explanation
of what<br>
you want, in stead of what doesn't work. In addition, give the
set of<br>
commands that bring you up to this point, and not only the
output of<br>
mdrun. That way we can probably see where you go astray.<br>
<br>
Cheers,<br>
<br>
Tsjerk<br>
<br>
<br>
On Wed, Jan 12, 2011 at 10:55 AM, mohsen ramezanpour<br>
<div>
<div class="h5"><<a moz-do-not-send="true"
href="mailto:ramezanpour.mohsen@gmail.com">ramezanpour.mohsen@gmail.com</a>>
wrote:<br>
><br>
> Dear Dr.Tsjerk<br>
><br>
> Before doing md for generating NPT, I did an EM,the
result was:<br>
> poteintial energy:-2.2611160*10^(6)<br>
> Max F=4.8960352*10^(4) on atom 5289<br>
> Besides I had done EM before on the same system,I
just add solvent by genbox<br>
> and Ions by genion.<br>
> the above result is for Energy minimization after
adding ions by genion.<br>
><br>
> I did what you said.but when I was generating NPT
equilibration<br>
> I recieved this massage:<br>
><br>
><br>
> Step 0, time 0 (ps) LINCS WARNING<br>
> relative constraint deviation after LINCS:<br>
> rms 8.387059, max 321.381958 (between atoms 5289 and
5290)<br>
> bonds that rotated more than 30 degrees:<br>
> atom 1 atom 2 angle previous, current, constraint
length<br>
> 5293 5294 74.4 0.1137 12.9330 0.1090<br>
> 5291 5293 59.1 0.1422 32.1605 0.1390<br>
> 5291 5292 103.5 0.1096 9.8747 0.1090<br>
> 5289 5291 89.5 0.1383 39.2022 0.1390<br>
> 5289 5290 85.7 0.1410 43.8439 0.1360<br>
> 5289 5287 85.4 0.1426 44.0196 0.1390<br>
> 5287 5288 90.2 0.1091 1.5178 0.1090<br>
> 5285 5287 88.7 0.1391 1.9186 0.1390<br>
> 5285 5286 41.8 0.1092 0.1322 0.1090<br>
> 5284 5293 87.2 0.1429 21.7425 0.1390<br>
> 5284 5285 92.4 0.1393 2.0880 0.1390<br>
> 5277 5278 79.1 0.1532 0.5213 0.1530<br>
> 5276 5284 63.0 0.1394 1.8946 0.1390<br>
> 5276 5277 79.2 0.1534 0.7278 0.1530<br>
> 5276 5275 79.9 0.1432 0.6036 0.1430<br>
> 5274 5275 82.0 0.1431 0.3189 0.1430<br>
> 5276 5272 82.1 0.1393 0.6113 0.1390<br>
> 5272 5273 74.2 0.1333 0.2251 0.1330<br>
> 5272 5270 77.7 0.1332 0.2428 0.1330<br>
> 5270 5271 46.5 0.1091 0.1682 0.1090<br>
> 5268 5270 36.9 0.1391 0.1854 0.1390<br>
> 5273 5266 41.4 0.1334 0.1933 0.1330<br>
> Wrote pdb files with previous and current coordinates<br>
> step 0Warning: 1-4 interaction between 5272 and 5293
at distance 22.443<br>
> which is larger than the 1-4 table size 2.400 nm<br>
> These are ignored for the rest of the simulation<br>
> This usually means your system is exploding,<br>
> if not, you should increase table-extension in your
mdp file<br>
> or with user tables increase the table size<br>
><br>
> Please let me know what can I do.<br>
> thanks in advance<br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
> On Thu, Jan 6, 2011 at 11:20 PM, Tsjerk Wassenaar
<<a moz-do-not-send="true"
href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>>
wrote:<br>
>><br>
>> Hi Mohsen,<br>
>><br>
>> I think rotating a molecule with editconf will
not rotate the box. Then<br>
>> again, if it did, it would result in a box
violating Gromacs requirements.<br>
>> Either way, it's not going to work like that.
Build a new box after<br>
>> rotation... And have a good look at what you're
actually trying now by<br>
>> taking the rotated system and stack it a few
times using genconf -nbox 2 2 2<br>
>><br>
>> Cheers,<br>
>><br>
>> Tsjerk<br>
>><br>
>> On Jan 6, 2011 7:22 PM, "mohsen ramezanpour"<br>
>> <<a moz-do-not-send="true"
href="mailto:ramezanpour.mohsen@gmail.com">ramezanpour.mohsen@gmail.com</a>>
wrote:<br>
>><br>
>> Dear Amit<br>
>> I entered these commands for rotating box:<br>
>> editconf -f conf.gro -o output.pdb
-rotate 0 0 25.4<br>
>> and then:<br>
>> editconf -f output.pdb -o newbox.pdb
-rotate 0 127.67548 0<br>
>> as a result my molecul is located out of box
totally,of course drug and<br>
>> protein are bind to eachother yet.<br>
>> thanks in advance for your attention and reply<br>
>><br>
>> On Tue, Jan 4, 2011 at 1:25 PM, Amit Choubey <<a
moz-do-not-send="true" href="mailto:kgp.amit@gmail.com">kgp.amit@gmail.com</a>>
wrote: ><br>
>> > Could you post the e...<br>
>><br>
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--<br>
</div>
</div>
Tsjerk A. Wassenaar, Ph.D.<br>
<br>
post-doctoral researcher<br>
Molecular Dynamics Group<br>
* Groningen Institute for Biomolecular Research and
Biotechnology<br>
* Zernike Institute for Advanced Materials<br>
University of Groningen<br>
The Netherlands<br>
<font color="#888888">--<br>
</font>
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