AMBER Archive (2008)

Subject: RE: AMBER: restraintmask - reference file is not working

From: Dirar Homouz (dirar_at_hotmail.com)
Date: Wed Dec 17 2008 - 03:41:00 CST

I tried using the fit mask and rms mask. However, the results are the same. To use the fit mask and rms mask, I used two different
control input files:

The first one with the position restraints:

 &cntrl
  imin = 0, ntb = 0,
  igb = 0, ntpr = 1, ntwx = 1,
  ntt = 3, gamma_ln = 1.0,
  tempi = 300.0, temp0 = 300.0
  nstlim = 100000, dt = 0.001,
  cut = 12.0,
  itgtmd= 1,
  tgtmdfrc= 100.0,
  ntr =1, ntrx=1, restraint_wt=10.0,
  tgtrmsmask='@2276-2299',
  restraintmask='@1-2299',
 /

And the second one without:

 &cntrl
  imin = 0, ntb = 0,
  igb = 0, ntpr = 1, ntwx = 1,
  ntt = 3, gamma_ln = 1.0,
  tempi = 300.0, temp0 = 300.0
  nstlim = 100000, dt = 0.001,
  cut = 12.0,
  itgtmd= 1,
  tgtmdfrc= 100.0,
  ntr =0, ntrx=1,
  tgtrmsmask='@2276-2299',
  tgtfitmask='@1-2299',
 /

In both cases the result is the same. RMS goes down, the restraint energy is non-zero. However, the structure is still fluctuating about
the inpcrd coordinates.

-Dirar

Date: Tue, 16 Dec 2008 20:05:03 -0500
From: carlos.simmerling_at_gmail.com
To: amber_at_scripps.edu
Subject: Re: AMBER: restraintmask - reference file is not working

then the mask is ok, but likely it's the best-fit is shifting the region to fit the refc without needing to change the conformation. try using a fit mask for the whole protein and rms mask just for that region.

On Tue, Dec 16, 2008 at 7:51 PM, Dirar Homouz <dirar_at_hotmail.com> wrote:

Hi Carlos again,

I'm sorry. I sent the information from the wrong output file. For the system i'm running the output file says:

     Mask @2276-2299; matches 24 atoms

The restraint energy is non-zero.

-Dirar

Date: Tue, 16 Dec 2008 19:38:14 -0500
From: carlos.simmerling_at_gmail.com
To: amber_at_scripps.edu

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 <dirar_at_hotmail.com> 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
"refc".

 I'm using the following input file

 ************************************************************
  &cntrl
   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
   ntr=1,
   ntrx=1,
   restraint_wt=100.0,
   restraintmask='@2276-2299',
  /
 ************************************************************

  with the following command

 $AMBERHOME/exe/sander -O -i pull.in -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?

-Dirar

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

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

_________________________________________________________________
Send e-mail faster without improving your typing skills.
http://windowslive.com/Explore/hotmail?ocid=TXT_TAGLM_WL_hotmail_acq_speed_122008
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu