Hi,
Instead of centering on an arbitrary part of your largest protein, try
centering on a part that is close to your 30-residue protein; once you
do that, omit the largest protein from the subseuqent image command.
For example, say your largest protein is residues 1-400, but residues
200-250 are the closest to the 30 residue protein:
trajin xxx.mdcrd
center :200-250 origin center
image origin center familiar !(:1-400)
trajout imaged.xxx.mdcrd netcdf
Hope this helps,
-Dan
On Sun, Jul 22, 2012 at 8:36 PM, Catein Catherine
<askamber23.hotmail.com> wrote:
>
> Dear Experts in AMBER group,
> I am doing a long simulation (using iwrap=1, with water box in rectangle size, 8 A from each side) for a protein complex with 3 protiens (400 residues + 100 residues + 30 residues)
> As the center of the complex is the 400 residues protein. As I used iwrap=1, I found the box shifted along the way. I tried several setting in doing ptraj for getting rmsd and rmsf data from the trajectory.
> (1) trajin xxx.mdcrd
center :1-530 origin
# all three protein in one goes
image origin center familiar
rms first out xxx.rms .CA
atomicfluct out xxx.nofactor .CA byres
average xxx_average.pdb pdb nobox
> I found this is wrong, as I got the averaged structure with all the proteins fragmented. I learnt it from the experts in AMBER archives that I have wrongly center all three proteins to center. So, I change the ptraj file as follows:
> (2) trajin xxx.mdcrd
center :1-400 origin
# only the largest and center part of the protein complex
image origin center familiar
rms first out xxx.rms .CA
atomicfluct out xxx.nofactor
.CA byres
average xxx_average.pdb pdb nobox
> I expecting it could works. However, when I have close look at the average structure, I found the averaged protein pdb file still contain fragmented chains. Most notably, the 30 residues protein (originally located at the top of the 400-residue protein), has now move to the bottom of the 400-residue protein. The rms file has starting values of 2-3 A, but jump to over 50A and back to 3 A along the trajectory. I learnt from achieve that we should the center with small part of the protein. So, I tried once as follows:
> (3) trajin xxx.mdcrd
center :1-100 origin
# small part of the largest and center part of the protein complex
image origin center familiar
rms first out xxx.rms .CA
atomicfluct out xxx.nofactor .CA byres
average xxx_average.pdb pdb nobox
> However, same results as (2) was obtained. I learnt from achieve that we can do stepwise centering. So, I tried once as follows:
> (3) trajin xxx.mdcrd
center :1-100 origin
# small part of the largest and center part of the protein complex
image origin center familiar
center :1-400 origin # small part of the largest and center part of
the protein complex
image origin center familiar
rms first out xxx.rms .CA
atomicfluct out xxx.nofactor .CA byres
average xxx_average.pdb pdb nobox
> However, same results as (2) was obtained.
>
> I am out of solution now. Could you mind to share your experiences with me how to get it work. It is a must that we should all the trajectory back to the box without redoing all the long simulations with a much larger water box size?
>
> Best regards,Catherine
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Lab Specialist
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jul 23 2012 - 09:30:03 PDT
