AMBER Archive (2009)

Subject: [AMBER] How to read md trajectory for each time slice as an input coordinate

From: Myeong Lee (
Date: Mon Jul 27 2009 - 03:16:47 CDT

Dear Amber users:

I had md trajectory, and I want to use the conformation of md trajectory
in each time slice as an input for the next single-point calculation
(doing md with nstlim=0 or doing minimization with maxcyc=1). Is there
any way that I can read md trajectory directory for each time frame?

 From Amber 10 tutorial I found the following option using -y inptraj
with (imin=5, maxcyc=1).

So, I did the following:
sander -i -p prmtop -c inpcrd -y mdcrd

(inpcrd file was the input coordinate for md simulation, and if I don't
add -c part, Amber gives error message.)
I'm not sure if Amber reads inpcrd (which is not my intention) or read
trajectory (mdcrd) as an input.

Also when I did the above, I've got the following error.

     Coordinate resetting (SHAKE) cannot be accomplished,
     deviation is too large
     NITER, NIT, LL, I and J are : 0 0 1 2 3

     Note: This is usually a symptom of some deeper
     problem with the energetics of the system.

Is this related to some mistakes in the command line or something wrong
in my md trajectory?

Also, I think maybe I can get inpcrd file for each time frame using
ptraj. Is it possible to extract inpcrd file from mdcrd file using ptraj?

Many thanks.


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