> Thanks for the tip. I didn't think to try it. But if I plan to do any > electrostatics I still need the tpr file right? So I would need to produce > a > top file. Mark, you mentioned making the S-S bonds by hand.
You can see that trjconv doesn't really need a .tpr because trjconv -h shows you that -s allows any structure file type as input. This is a general GROMACS phenomenon. >>You still won't get them bonded with this procedure... you need a .top >>file with S-S bonds, and you get that by producing one by hand or using >>pdb2gmx. > > Could you or anyone else point me in the right direction to do this? I'm a bit hamstrung because I don't know a) why you are trying to make S-S bonds from a structure that has sulfurs more than 2A apart b) where this structure came from c) whether you have tried the second procedure I suggested in the email you quote http://www.gromacs.org/pipermail/gmx-users/2007-July/028337.html d) whether you have tried the other suggestion I made http://www.gromacs.org/pipermail/gmx-users/2007-July/028356.html Making the topology by hand requires you to read chapter five of the manual thoroughly and then go through a working topology with the manual at hand so that you understand all the bits. Only then could you hope to make a S-S topology by hand, and then you'll probably run into hassles with things breaking when you try to minimize with it. Much easier will be c) or d) above. Mark _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
