> Hello Mark, > > 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). > > 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.
Fine, but if I remember the discussion accurately, both of the above didn't have the sulfur atoms that you think should be bonded at a distance consistent with a single bond. If not, why not? > c) The structure was already minimized. That's not the point. If you have sulfurs that are too far for pdb2gmx to create a disulfide bond, then one way to get them close enough is to force the minimizer to put them close. > 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. So either you're doing the same thing wrong, or the same disulfide(s) distances are not consistent with disulfide bonds. > 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. It sounds like you should be using -merge and -ss and specbond.dat correctly on a structure file that has the S-S distances corresponding approximately to the entries in specbond.dat If not, you will have problems. 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
