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>Please report this to the mailing list (<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>)<br>
<br>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 class="gmail_quote">On Thu, Jun 26, 2008 at 10:26 AM, Tsjerk Wassenaar <<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</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;">
Hi Ram,<br>
<br>
Check the option -merge of pdb2gmx.<br>
<br>
Cheers,<br>
<br>
Tsjerk<br>
<div><div></div><div class="Wj3C7c"><br>
On Thu, Jun 26, 2008 at 6:11 AM, rams rams <<a href="mailto:rams.crux@gmail.com">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 disulphide<br>
> bond between two fragments. If I keep the two fragments as separate objects<br>
> while preparing the pdb file (using TER between the two fragments), gromacs<br>
> is not asking for the formation of a disulphide bond. If I keep them as a<br>
> single object while preparing the input pdb, gromacs could recognize the<br>
> disulphide bond but while running the energy minimization its complaining<br>
> that the distances are too close.<br>
><br>
> Is there any way to handle these ? I am also thinking like keep them as<br>
> separate objects and imposing positional restraints on both the 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>
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<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>
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