AMBER Archive (2008)

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

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Tue Dec 16 2008 - 19:05:03 CST

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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>
>
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