AMBER Archive (2008)

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

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Wed Dec 17 2008 - 07:19:25 CST

sounds like it should be working. does the initial/final rms match what you
get in the viz program that you are using the view the trajectory?
I just don't have enough detail to make any more suggestions. you definitely
don't want to use ntr=1 with this.

On Wed, Dec 17, 2008 at 4:41 AM, Dirar Homouz <dirar_at_hotmail.com> wrote:

> 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
>
>
>
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