On Mon, 2006-10-30 at 15:27 +0100, Sergey Samsonov wrote:
> Dear Mr. Roitberg,
>
> thank you very much for the answer!
>
> Adrian Roitberg wrote:
> > Sergey Samsonov wrote:
> >
> > Sergey,
> > First, I expect that the output traj will have box info, unless you
> > explicitely write nobox there.
> Yes, the output traj has the box info.
> >
> > More importantly, what top file are you using to visualize ?
> > You should not be using the original one with all the waters, since
> > your new trajectory only has ten of them.
> Indeed I used the same one and it was the mistake I suppose. Now I
> created the top file from the pdb which consisted of the protein,
> counterions and 10 water molecules, put also setBox in startleap.
> Unfortunately I saw almost the same in VMD (now there are long bonds but
> within the certain space, probably the space of the box).
> >
> > So, create a new top file with just ten waters, out of a pdb file, and
> > look again.
> Should I do that just for water molecules without protein and counterions?
The number of closest water molecules may different in different snapshots. I expect A topology file won't be able to fit all snapshots.
You may try output each conformation to PDB files directly. However, I
am not sure ptraj can do this or not.
Mingfeng
> Thank you very much for the help!
>
> Sergey
> >
> > When things like this happen, it is always useful to LOOK into the
> > mdcrd file to see what numbers are in there.
> >
> > Cheers
> > a.
> >
> >
>
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Received on Wed Nov 01 2006 - 06:07:19 PST
