Hello Mark,<br><br>a) I know for sure that the structure has a given number of disulfide bonds. I have several other Gromacs simulations where the bonds are present initially and stay bonded; my current problem has to do with converting this Amber trajectory to Gromacs format (which I'm doing becuase I'm most familiar with gromacs tools right now).
<br><br>b)This structure came from a pdb crystal structure orginally. It was properly minimized, equilibrated to 300K and simulated in a box of water for about 10ns. <br><br>c) The structure was already minimized.<br><br>
d) The only usuable structure file from Amber for gromacs conversion is in the pdb format, which is what I used. I did use a pdb frame from later in the trajectory but I get the same results.<br><br>The structure consists of 4 chains with disulfide bonds in several places and some between chains. When I use the -merge option, I get problems with the chains. When I use the -ignh option, all the cysteines are protonated (which is not what should be happening). If I use the -ss option...nothing happens.
<br><br>Sorry for the late reply,<br>Russell Green<br><br><div><span class="gmail_quote">On 7/2/07, <b class="gmail_sendername">Mark Abraham</b> <<a href="mailto:mark.abraham@anu.edu.au">mark.abraham@anu.edu.au</a>> wrote:
</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">> Thanks for the tip. I didn't think to try it. But if I plan to do any<br>> electrostatics I still need the tpr file right? So I would need to produce
<br>> a<br>> top file. Mark, you mentioned making the S-S bonds by hand.<br><br>You can see that trjconv doesn't really need a .tpr because trjconv -h<br>shows you that -s allows any structure file type as input. This is a
<br>general GROMACS phenomenon.<br><br>>>You still won't get them bonded with this procedure... you need a .top<br>>>file with S-S bonds, and you get that by producing one by hand or using<br>>>pdb2gmx.
<br>><br>> Could you or anyone else point me in the right direction to do this?<br><br>I'm a bit hamstrung because I don't know<br>a) why you are trying to make S-S bonds from a structure that has sulfurs<br>
more than 2A apart<br>b) where this structure came from<br>c) whether you have tried the second procedure I suggested in the email<br>you quote <a href="http://www.gromacs.org/pipermail/gmx-users/2007-July/028337.html">http://www.gromacs.org/pipermail/gmx-users/2007-July/028337.html
</a><br>d) whether you have tried the other suggestion I made<br><a href="http://www.gromacs.org/pipermail/gmx-users/2007-July/028356.html">http://www.gromacs.org/pipermail/gmx-users/2007-July/028356.html</a><br><br>Making the topology by hand requires you to read chapter five of the
<br>manual thoroughly and then go through a working topology with the manual<br>at hand so that you understand all the bits. Only then could you hope to<br>make a S-S topology by hand, and then you'll probably run into hassles
<br>with things breaking when you try to minimize with it. Much easier will be<br>c) or d) above.<br><br>Mark<br><br>_______________________________________________<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">
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