Hi,<br><br>If I use -ignh, that will ignore all the hydrogens in my input. And these hydrogens are added by the <a href="http://gromacs.in">gromacs.in</a> the first step of creating the top file.<br><br>Ram.<br><br><div class="gmail_quote">
On Thu, Jun 26, 2008 at 3:34 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
<br>
rams rams wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="Ih2E3d">
Dear Tsjerk,<br>
<br>
Thanks for the suggestion but when I use -merge command it says segmentation error. Let me put the problem in a more elaborated way.<br>
<br>
I am running this simulation on insulin. It has two chains "a" and "b" which are independent fragments but there are two inter disulphide bonds between the two chains. If I keep the two chains as a single molecule (as -merge command does) gromacs could recognize the inter dishlphide bonds but while running the following error appears:<br>
<br>
396 398 113.3 0.1470 0.2974 0.1470<br>
398 399 93.1 0.1530 0.4267 0.1530<br>
399 400 45.5 0.1230 0.1693 0.1230<br>
399 401 46.5 0.1330 0.1881 0.1330<br>
Step= 2, Dmax= 5.0e-03 nm, Epot= -3.06153e+22 Fmax= inf, atom= 25<br>
-------------------------------------------------------<br>
Program mdrun, VERSION 3.3.1<br>
Source code file: nsgrid.c, line: 226<br>
<br>
Range checking error:<br>
Explanation: During neighborsearching, we assign each particle to a grid<br>
based on its coordinates. If your system contains collisions or parameter<br>
errors that give particles very high velocities you might end up with some<br>
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot<br>
put these on a grid, so this is usually where we detect those errors.<br>
Make sure your system is properly energy-minimized and that the potential<br>
energy seems reasonable before trying again.<br>
<br>
Variable ci has value -2147483648. It should have been within [ 0 .. 1000 ]<br></div>
Please report this to the mailing list (<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a> <mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>>)<br>
<br>
</blockquote>
<br>
When do you get this error (i.e., minimization, equilibration, production)? Usually this type of error comes up from a poorly minimized/equilibrated structure. <br>
I agree with Tsjerk that using -merge is the right way to form your disulfide, so I assume something else is going wrong during your system preparation. If you'd like to provide details on what you're doing in terms of minimization/equilibration, and the contents of the relevant .mdp files, we may be able to detect problems.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="Ih2E3d">
Where as, if I keep these two as separate molecules it couldnt recognize the two inter disulphide bonds but its running. Now it is adding hydrogens to the sulhur atoms.<br>
<br>
Is there any way to fix this problem ? Is there any way to edit the topology file to remove the added hydrogen atoms ?<br>
<br>
Thanks<br>
Ram.<br>
<br></div><div class="Ih2E3d">
On Thu, Jun 26, 2008 at 10:26 AM, Tsjerk Wassenaar <<a href="mailto:tsjerkw@gmail.com" target="_blank">tsjerkw@gmail.com</a> <mailto:<a href="mailto:tsjerkw@gmail.com" target="_blank">tsjerkw@gmail.com</a>>> wrote:<br>
<br>
Hi Ram,<br>
<br>
Check the option -merge of pdb2gmx.<br>
<br>
Cheers,<br>
<br>
Tsjerk<br>
<br>
On Thu, Jun 26, 2008 at 6:11 AM, rams rams <<a href="mailto:rams.crux@gmail.com" target="_blank">rams.crux@gmail.com</a><br></div><div class="Ih2E3d">
<mailto:<a href="mailto:rams.crux@gmail.com" target="_blank">rams.crux@gmail.com</a>>> wrote:<br>
> Dear Gromacs users,<br>
><br>
> Is there any way to handle the disulphide bond formed between two<br>
> independent fragments of a protein ? Precisely it is an inter<br>
disulphide<br>
> bond between two fragments. If I keep the two fragments as<br>
separate objects<br>
> while preparing the pdb file (using TER between the two<br>
fragments), gromacs<br>
> is not asking for the formation of a disulphide bond. If I keep<br>
them as a<br>
> single object while preparing the input pdb, gromacs could<br>
recognize the<br>
> disulphide bond but while running the energy minimization its<br>
complaining<br>
> that the distances are too close.<br>
><br>
> Is there any way to handle these ? I am also thinking like keep<br>
them as<br>
> separate objects and imposing positional restraints on both the<br>
sulphur<br>
> atoms. Is it all right to do that way ?<br>
><br>
> Please suggest me some thing how to handle these ?<br>
><br>
> Ram.<br>
><br>
> _______________________________________________<br>
> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br></div>
<mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><div class="Ih2E3d"><br>
> <a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>
> Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a><br>
before posting!<br>
> Please don't post (un)subscribe requests to the list. Use the<br>
> www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a><br></div>
<mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>>.<div class="Ih2E3d"><br>
> Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
><br>
<br>
<br>
<br>
--<br>
Tsjerk A. Wassenaar, Ph.D.<br>
Junior UD (post-doc)<br>
Biomolecular NMR, Bijvoet Center<br>
Utrecht University<br>
Padualaan 8<br>
3584 CH Utrecht<br>
The Netherlands<br>
P: +31-30-2539931<br>
F: +31-30-2537623<br>
_______________________________________________<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br></div>
<mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><div class="Ih2E3d"><br>
<a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before<br>
posting!<br>
Please don't post (un)subscribe requests to the list. Use the<br>
www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a><br></div>
<mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>>.<div class="Ih2E3d"><br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
<br>
<br></div>
------------------------------------------------------------------------<div class="Ih2E3d"><br>
<br>
_______________________________________________<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
</div></blockquote>
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Graduate Research Assistant<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<div><div></div><div class="Wj3C7c"><br>
<br>
_______________________________________________<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
</div></div></blockquote></div><br>