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?
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.
>
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Wed Nov 01 2006 - 06:07:13 PST
