you are calculating the RMSD (not RSM) from the first frame of the
trajectory,
and that changes for each run. you probably want to calculate RMSD
from the same set of coordinates for each of the trajectories. you
didn't say what reference structure you want to use.
it looks like you need to read the ptraj documentation and learn how
to use this program.
===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
Stony Brook University Web: http://comp.chem.sunysb.edu/carlos
Stony Brook, NY 11794-5115 E-mail: carlos.simmerling.stonybrook.edu
===================================================================
bybaker.itsa.ucsf.edu wrote:
>Hello, Amber:
>
>I try to extract the RSM information from the MD runs on my protein
>model. Due to the limited computer resource, my first MD run was
>disrupted. I continued the runs from the previous .rst files. The MD
>simulation was completed with 4 continuous runs. Four .crd files were saved.
>
>Here is how I did to extract the rsm values:
>
>model1-3md1CA-rms.in
>trajin model1-3-md1.crd
>rms first out model1-3md1-backbone.rms .CA time 0.2
>strip :WAT
>go
>
>
>model1-3md2CA-rms.in
>trajin model1-3-md2.crd
>rms first out model1-3md2-backbone.rms .CA time 0.2
>strip :WAT
>go
>
>
>
>model1-3md2aCA-rms.in
>trajin model1-3-md2a.crd
>rms first out model1-3md2a-backbone.rms .CA time 0.2
>strip :WAT
>go
>
>
>
>model1-3md2bCA-rms.in
>trajin model1-3-md2b.crd
>rms first out model1-3md2b-backbone.rms .CA time 0.2
>strip :WAT
>go
>
>
>
>When I check the outputs, something is very strange. The numbers all
>start from 0.00 and gradually go up:
>
>In ‘model1-3md1-backbone.rms’, the values are: 0.0000, 0.7285, -----
>1.1585, ----1.4267, ----1.72762 (total 46 sets).
>
>In ‘model1-3md2-backbone.rms’, the values are: 0.0000, 0.81433, ----,
>1.04982, ---1.26905, ---1.33873 (total 18 sets).
>In ‘model1-3md2a-backbone.rms’, the values are: 0.0000, 0.73119,
>---1.00127, ---1.10160, ---- 1.48751, ---- 1.17671 (total 18 sets).
>
>In ‘model1-3md2b-backbone.rms’, the values are: 0.0000, 0.74736, ----
>1.07326, ---1.20359, ---1.03816, ----- 1.07571 (total 50 sets).
>
>
>The RSM values should be consistant from the previous run. What happened?
>How can I get the right RSM values from the .crd files ? I use Amber7.
>The comment used in ptraj is: ptraj model1-3.prmtop < model1-3md1CA-rms..in
>
>Thank you for your help.
>
>Bo
>
>
>-----------------------------------------------------------------------
>The AMBER Mail Reflector
>To post, send mail to amber.scripps.edu
>To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Oct 31 2004 - 06:53:01 PST
