AMBER Archive (2006)

Subject: Re: AMBER: Closest(closest water)

From: Sergey Samsonov (
Date: Wed Nov 01 2006 - 02:38:55 CST

Finally I managed to do that. Mr. Roitberg, you were absolutely right
but somehow I didn't manage at first. Thank you very much for the help!

So I took one of the shots from the trajectory and converted it to pdb
file with AMBPDB, then I modified this pdb file and left only 10 water
created the new topology file in xleap from this pdb (just loaded the
pdb and saved the parameters without doing anything esle, since the
coordinates are
already in the trajectory file and one shouldn't even setBox for the new
topology). Then in VMD I used new topology file with the processed
trajectory and
everything went fine.


Mingfeng Yang wrote:
> 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.
>> -----------------------------------------------------------------------
>> The AMBER Mail Reflector
>> To post, send mail to
>> To unsubscribe, send "unsubscribe amber" to
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to
> To unsubscribe, send "unsubscribe amber" to

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to