AMBER Archive (2004)

Subject: AMBER: RSM & ptraj

From: bybaker_at_itsa.ucsf.edu
Date: Sun Oct 31 2004 - 01:13:10 CDT

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

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