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 - 13:51:35 CST

maybe you can send me the inputs (inpcrd, prmtop, mdin and mdout) directly
and I'll look at it and see what sander is doing.
if it didn't read the refc it should not get an rmsd value, so I'm not sure
what's wrong.

On Wed, Dec 17, 2008 at 2:40 PM, Dirar Homouz <dirar_at_hotmail.com> wrote:

> Hi Carlos,
>
> The rmsd that I get from sander output is:
>
> Current RMSD from reference: 0.094
> Current target RMSD: 0.000
>
>
>
> The rmsd that I get from vmd is 8.87.
>
> It looks like the reference file is not read. Am I defining it in the wrong
> way?
>
> -Dirar
> ------------------------------
> Date: Wed, 17 Dec 2008 08:19:25 -0500
>
> From: carlos.simmerling_at_gmail.com
> To: amber_at_scripps.edu
> Subject: Re: AMBER: restraintmask - reference file is not working
>
> 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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