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
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