AMBER Archive (2007)

Subject: Re: AMBER: image command

From: Petr Kulhanek (kulhanek_at_chemi.muni.cz)
Date: Wed Jan 10 2007 - 02:45:45 CST

Hello,

the order of commands is incorrect. It should be:

trajin ../name_md1.mdcrd
trajin ../name_md2.mdcrd
trajout ../name.pdb pdb

center :1-24
image familiar

rms first out rms @P,O3',O5',C3',C4',C5'

go

The reason is that you have to image your system BEFORE rms. rms command
reorient the system of coordinates while image command still works in
original system orientation.

With regards,
        Petr

Thomas Cheatham wrote:
>>I ran a MD simulation using a truncated octahedron box. Then I imaged the
>>trajectory using the following input files for the ptraj command:
>>
>>trajin ../name_md1.mdcrd
>>trajin ../name_md2.mdcrd
>>trajout ../name.pdb pdb
>>rms first out rms @P,O3',O5',C3',C4',C5'
>>center :1-24
>>image familiar
>>go
>
>
> The above script will center to the box center (boxx/2, boxy/2, boxz/2)
> and then image (to the closest spherical shape).
>
>
>>trajin ../name_md1.mdcrd
>>trajin ../name_md2.mdcrd
>>trajout ../name.pdb pdb
>>rms first out rms @P,O3',O5',C3',C4',C5'
>>center :1-24
>>image origin center familiar
>>go
>
>
> This script will center to the box center, but image via the "origin"
> (i.e. box center is assumed to locate at 0,0,0; this will leave the solute
> (:1-24) at the edge of the box.
>
>
>>The final trajectories show many overlap between water molecules.
>
>
> This I do not understand; what waters are overlapping; or equivalently,
> how are you seeing that the waters overlap? This should only happen if
> the box information is incorrect (in the mdcrd files unless it was
> overridden with the box command).
>
>
>>So I tryied to use the IWRAP option in the MD run:
>>
>
> ...
>
>>However, at the beginning of the simulation, my molecule is placed outside
>>the box and the center command of ptraj (please see below) doesn't modify
>>the solute position.
>>
>>trajin ../name_md1.mdcrd
>>trajin ../name_md2.mdcrd
>>trajout ../PDB_traj/name_md_centre.pdb PDB
>>center :1-24
>>go
>
>
> The center command above only shifts the relative position of the ENTIRE
> box, i.e. it places the center of mass of residues 1-24 at the box center,
> i.e. boxx/2, boxy/2, boxz/2.
>
> The IWRAP in sander and image in ptraj are effectively equivalent in the
> usage as per the first ptraj script you specified...
>
> If you are still stuck, you can e-mail me directly (with the prmtop and
> part of ../name_md1.mdcrd) and I can try to help decipher.
>
> --tom
>
> tec3 @ utah.edu
>
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-- 
##################################################
   Petr Kulhanek
  ------------------------------------------------
   E-mail: kulhanek_at_enzim.hu
   WWW: http://www.ncbr.chemi.muni.cz/~kulhanek
  ------------------------------------------------
   Institute of Enzymology
   Biological Research Center
   Hungarian Academy of Sciences
   Karolina ut 29, H-1113 Budapest
   Hungary
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