AMBER Archive (2006)

Subject: Re: AMBER: Closest(closest water)

From: Sergey Samsonov (sergeys_at_biotec.tu-dresden.de)
Date: Mon Oct 30 2006 - 08:27:40 CST

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.
>
>

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