Hi Carlos,
I really appreciate your help. I was not enumerating the atoms correctly. It work now fine.
Thanks,
Dirar
Date: Thu, 18 Dec 2008 07:14:27 -0500
From: carlos.simmerling.gmail.com
To: amber.scripps.edu
Subject: Re: AMBER: restraintmask - reference file is not working
Dirar,
after looking at your files, it seems that the region of atoms from your rmsmask (2276-2299) is the same in both structures, that's why the rmsd is zero. there is a region that differs, but it's at around atom # 3100, and not 2276. also, when I did the align and rmsd (different selections, like your sander input) in VMD I get 0 rmsd, not 8.87 like your earlier mail said. maybe these aren't the right coordinates?
carlos
On Wed, Dec 17, 2008 at 2:51 PM, Carlos Simmerling <carlos.simmerling.gmail.com> wrote:
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.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.gmail.com
To: amber.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.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.gmail.com
To: amber.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.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.gmail.com
To: amber.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.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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Received on Fri Dec 19 2008 - 01:21:18 PST
