Dear <br>
yes,I did my work with pdb files.<br>
these are my commands after generating complex.gro and complex.top(according to Enzyme/Drug tutorial)<br>
editconf -f complex.gro -o box.pdb -d 1.0 -angles 90 90 90 ;for generating a typical rectangular box<br>
editconf -f box.pdb -o first-box -vec 5 5 20 -translate 0 0 4 ;to make a rectangular box with wanted length<br>
editconf -f first-box -o second-box -rotate 0 0 6 ;to rotate box around it's z axis<br>
editconf -f second-box -o third-box -rotate 0 127 0 ;to rotate box around it's y axis<br>
genbox -cp third-box -cs spc216 -p complex.top -o solvent.pdb ;to make solvate <br>
grompp -f ion.mdp -c solvent.pdb -o solvent-ion.tpr -p complex.top<br>
genion -s solvent-ion.tpr -o solvent-ion.pdb -p complex.top -neutral -nn 3<br>
grompp -f minim.mdp -c solvent-ion.pdb -o solvent-ion-EM.tpr -p complex.top<br>
mdrun -v -deffnm solvent-ion-EM<br>
grompp -f npt.mdp -c solvate-ion-EM.pdb -o NPT.tpr<br>
mdrun -v -deffnm NPT<br><br><div class="gmail_quote">On Wed, Jan 12, 2011 at 2:17 PM, Tsjerk Wassenaar <span dir="ltr"><<a 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 started off with a pdb file or so. What commands (full command<br>
lines) did you issue to get to the point where you are?...<br>
<br>
Tsjerk<br>
<br>
On Wed, Jan 12, 2011 at 11:37 AM, mohsen ramezanpour<br>
<div><div></div><div class="h5"><<a href="mailto:ramezanpour.mohsen@gmail.com">ramezanpour.mohsen@gmail.com</a>> wrote:<br>
> 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<br>
> can fit the pulling line along one box axis.<br>
> besides I have to pull drug not at direction which connect COM of protein<br>
> and drug,but it is better to pull it along line which connects drug to<br>
> a residue inside of hole.<br>
><br>
> I rotated box with editconf ,solvated system with genbox,neutralized with<br>
> genion,<br>
> now I want to generate NPT and then generating configuration as umbrella<br>
> sampling tutorial.<br>
><br>
><br>
><br>
> On Wed, Jan 12, 2011 at 1:53 PM, Tsjerk Wassenaar <<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>> wrote:<br>
>><br>
>> 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>
>> <<a 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<br>
>> > 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 href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>><br>
>> > 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<br>
>> >> 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<br>
>> >> 2 2 2<br>
>> >><br>
>> >> Cheers,<br>
>> >><br>
>> >> Tsjerk<br>
>> >><br>
>> >> On Jan 6, 2011 7:22 PM, "mohsen ramezanpour"<br>
>> >> <<a 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 href="mailto:kgp.amit@gmail.com">kgp.amit@gmail.com</a>><br>
>> >> wrote: ><br>
>> >> > Could you post the e...<br>
>> >><br>
>> >> --<br>
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>><br>
>><br>
>><br>
>> --<br>
>> 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>
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<br>
<br>
<br>
--<br>
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>
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</div></div></blockquote></div><br>