> Hmm...well the thing is, I just need a .tpr file (which I was getting with > pdb2gmx followed by grompp) so I can convert an amber pdb trajectory to > xtc > format. The simulation is already complete, I'm just converting it, but of > course the atoms from the tpr need to match those of the trajectory. So > should I still be doing something different other than my idea to change > the > residue names of the .itp files, as mentioned previously? Sorry for some > of > my ignorance, I'm still new with much of this. Thanks for all the > suggestions and input!
So take a frame from the trajectory which you know has sensible disulfide bond lengths, embed that in a structure file using some Amber tool, and use that as your input to pdb2gmx. 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
