May not be a residue, just pick an atom in the center residue. Have a try and hope you succeed.
Yang Ye Thanks for Tsjerk's input. Rob, please make sure that that portion of DNA is always binding together. Since you have a ssDNA, just center the center residue. mol was a non-existing option. It sounds meaningful =) Just use whole, please. Regards, Yang Ye Tsjerk Wassenaar wrote: > Hi Robert, > > Maybe it's a bit nasty, but you may try the following, assuming that > your ends stay a bit together: > > 1. Translate your system such that the last atom of chain A is > centered in the _rectangular_ unitcell. > 2. Generate a .tpr file from the translated system > 3. Convert the .tpr to .pdb > > Gromacs places molecules in the box based on the first atom. Since > you're dealing with DNA, your chains will be head to tail. Placing the > tail of chain A in the center would mean that there's a periodic image > of your chain B which has its first atom in the center. This image > will be chosen during the generation of the .tpr file. Converting the > .tpr to .pdb should give both chains close to each other. Processing > the trajectory will be another thing... > > Tsjerk > > > On 3/15/07, Robert Johnson <[EMAIL PROTECTED]> wrote: >> I made an index file that contained the middle portion of the DNA >> strand. I then used the -center option to center this middle portion >> in the box and then outputted the entire molecule. However, the >> molecule still appears broken. What is this -pbc mol option? That >> doesn't seem to be one of the available pbc options. >> Bob >> >> On 3/14/07, Yang Ye <[EMAIL PROTECTED]> wrote: >> > A rather simple but effective way is to make an index which >> contains 1/4 >> > of your protein file. Use trjconv with -center tric -pbc whole/mol to >> > center that 1/4 of your protein and output the whole protein. >> > >> > >> > Tsjerk Wassenaar wrote: >> > > Hi Bob, >> > > >> > > You could try -pbc cluster. If that doesn't work, it'll be >> difficult. >> > > The option -pbc nojump will only work on continuous trajectories. >> > > >> > > Cheers, >> > > >> > > Tsjerk >> > > >> > > On 3/14/07, Robert Johnson <[EMAIL PROTECTED]> wrote: >> > >> Hello everyone, >> > >> I'm trying to visualze the conformations of a ssDNA molecule >> obtained >> > >> from a >> > >> REMD trajectory. As expected, there are parts of the simulation >> where >> > >> the >> > >> oligomer is broken due to the PBC wrapping. I've been trying to fix >> > >> this with >> > >> trjconv. However, the -pbc nojump option doesn't work - it actually >> > >> makes the >> > >> broken portions of the molecule worse and gives a terribly >> distorted >> > >> trajectory. Since the REMD trajectory isn't continuous (i.e. >> there are >> > >> instaneous jumps in the coordinates associated with REMD swaps), >> the >> > >> nojump >> > >> option may have problems. Does anyone know of any other way or >> other >> > >> tools that >> > >> I could use to reassemble my broken DNA strand? >> > >> Thanks, >> > >> Bob Johnson >> > >> _______________________________________________ >> > >> gmx-users mailing list [email protected] >> > >> http://www.gromacs.org/mailman/listinfo/gmx-users >> > >> 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 >> > >> >> > > >> > > >> > >> > _______________________________________________ >> > gmx-users mailing list [email protected] >> > http://www.gromacs.org/mailman/listinfo/gmx-users >> > 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 >> > >> _______________________________________________ >> gmx-users mailing list [email protected] >> http://www.gromacs.org/mailman/listinfo/gmx-users >> 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 >> > > _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users 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
