RE: AMBER: restraintmask - reference file is not working

From: Dirar Homouz <>
Date: Tue, 16 Dec 2008 18:45:44 -0600

Hi Carlos,

In the output file. It says

     Mask :2276-2299; matches 0 atoms

The restraint energy is 0.0. What does that mean?


Date: Tue, 16 Dec 2008 19:38:14 -0500
Subject: Re: AMBER: restraintmask - reference file is not working

look in the sander output- does sander recognize the restraints? does it list the correct # of atoms matching the mask? if so, is the restraint energy non-zero?
are the atoms shifted as a group? meaning even if they are shifted, is it possible that the best-fit process shifts them back to perfect alignment to refc? if so, perhaps you want a separate fit mask and rms mask.

check these, it's the important information you need to know what's going on.

On Tue, Dec 16, 2008 at 7:05 PM, Dirar Homouz <> wrote:

Dear Amber users,

I'm trying to pull a certain structure using restraintmask from an initial structure
defined by the input file "inpcrd" to a final structure defined by reference file

 I'm using the following input file

   imin = 0, ntb = 0,
   igb = 0, ntpr = 100, ntwx = 100,
   ntt = 3, gamma_ln = 1.0,

   tempi = 300.0, temp0 = 300.0
   nstlim = 100000, dt = 0.001,
   cut = 12.0

  with the following command

 $AMBERHOME/exe/sander -O -i -o pull.out -c inpcrd -p prmtop -r
 rst -ref refc

 The inpcrd file is different from the refc file. The last 24 atoms are

 shifted from their initial positions.

The code runs fine. However, it doesn't move the structure to the
coordinates defined by the refc file. I'm not sure why is the refc file
is not recognized?


Send e-mail anywhere. No map, no compass. Get your HotmailŪ account now.

Send e-mail faster without improving your typing skills.
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
Received on Wed Dec 17 2008 - 01:23:10 PST
Custom Search