AMBER Archive (2007)

Subject: RE: AMBER: problem with calculating RMSD

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Wed Apr 18 2007 - 11:03:37 CDT


Dear Tri,
 
The following will do what you want in Carnal:
 
FILES_IN
  PARM p1 1LDY_analogy.prmtop;
  STATIC t1 1LDY_analogy.prmcrd;
  STREAM s1 ../1LDY_prod_300K_10ps.mdcrd.bz2;
 
FILES_OUT
  TABLE tab1 1LDY_pav_full_rms_per_res_1_to_756_analogy.tab;
  
DECLARE
  GROUP solute (RES 1-756);
  RMS fit1 FIT solute s1 t1;
  
OUTPUT
  TABLE tab1 fit1%residues;
 
END
 
Carnal is no longer supported however so unless you have it lying around you
will have to use ptraj. You can almost certainly do the same thing in ptraj
I just have never attempted it. Take a look at the ptraj section of the
manual it should be fairly easy to work out how to do it. Some example
scripts for using ptraj are also included on the amber tutorials
http://amber.scripps.edu/tutorials/
 
Good luck...
 
Ross
 
/\
\/
|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk <http://www.rosswalker.co.uk/> | PGP Key
available on request |

Note: Electronic Mail is not secure, has no guarantee of delivery, may not
be read every day, and should not be used for urgent or sensitive issues.
 

  _____

From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
tri nam Vo
Sent: Wednesday, April 18, 2007 01:23
To: amber_at_scripps.edu
Subject: Re: AMBER: problem with calculating RMSD

Dear, Gustavo
Thank for your helping. I've solved that problem.
But, I'm trying to study the stability of protein. So, could you tell me how
to compare the structures before and after MD by residures? I'd like to know
which residure have change in position. Thanks a lot.

Gustavo Seabra <gustavo.seabra_at_gmail.com> wrote:

The tutorial uses ntwx=5000. If you just changed nstlim to 5000, and did not
touch ntwx, you only get one structure in the trajectory file (if any at
all).

Gustavo.

tri nam Vo wrote:

Dear everyone,
I've done after the tutorial of amber8 at page
http://amber.scripps.edu/tutorial/integrase/loop11.htm.
Reimaging trajectory input:
trajin wt1mg_eq.crd
center :1-154
image center familiar
rms first out wt1mg_eq_rms.out :3-152_at_CA
trajout wt1mg_eq_nice.crd nobox
save this input and call it "ptraj.in" and then run ptraj as follows:
$ ptraj wt1mg.parm7 ptraj.in
I just test so I did just nstlim=5000 (instead of 50000 as in tutorial).
And I've received out file with just one line: 1.00 0.00000
Could anyone tell me the reason of it?
By the way, I want to learn how to compare the structure of my protein by
residure before and after MD. (I want to know which residure have change in
position).
Thank for your helping.
  _____

Ahhh...imagining that irresistible "new car" smell?
Check out new cars at Yahoo! Autos.
<http://us.rd.yahoo.com/evt=48245/*http://autos.yahoo.com/new_cars.html;_ylc
=X3oDMTE1YW1jcXJ2BF9TAzk3MTA3MDc2BHNlYwNtYWlsdGFncwRzbGsDbmV3LWNhcnM->

  _____

Ahhh...imagining that irresistible "new car" smell?
Check out new
<http://us.rd.yahoo.com/evt=48245/*http://autos.yahoo.com/new_cars.html;_ylc
=X3oDMTE1YW1jcXJ2BF9TAzk3MTA3MDc2BHNlYwNtYWlsdGFncwRzbGsDbmV3LWNhcnM-> cars
at Yahoo! Autos.

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu