Re: [AMBER] Does anyone knows how to generate an ired vector

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Wed, 11 Dec 2013 20:57:49 -0700

Hi,

On Wed, Dec 11, 2013 at 4:49 PM, 肖立 <xiaoli19871216.gmail.com> wrote:

> Hi, Dan:
> Thank you for your answer. However, in our problem, we need to analyze
> the autocorrelation function of N-H bond over almost 500 residues. Hence,
> it seems that it is not a clever way if we type 500 lines to generate these
> vectors. Do you have a cleverer way to do it?
>

For something like that I usually use the 'select' command in cpptraj,
which will output a list of atom numbers corresponding to a mask preceded
by 'Selected=' in STDOUT. Given that in Amber the H atom always follows the
N atom (+1) you can do something like (bash):

cat > cpptraj.in <<EOF
parm prmtop.parm7
select @%N&!:GLY,PRO
EOF
NATOMS=`cpptraj -i cpptraj.in | grep "Selected="`
echo $NATOMS

The mask expression literally means "select atom type N and not residues
GLY or PRO. You could modify this expression to only select certain
residues etc. Then you can iterate over the atom numbers in NATOMS like so
(bash again):

rm cpptraj.in
V=0
for N in $NATOMS ; do
   if [[ "$N" != "Selected=" ]] ; then
    ((H = $N + 1))
    echo "vector v$V .$N ired @$H" >> cpptraj.in
    ((V++))
  fi
done

Hope this helps,

-Dan


> Thanks a lot!
> Li
>
>
> On Wed, Dec 11, 2013 at 3:10 PM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
>
> > Hi,
> >
> > The IRED procedure involves defining the IRED vectors, creating an IRED
> > matrix, diagonalizing the IRED matrix, then finally performing the IRED
> > analysis. The following is an example for performing IRED analysis in
> > CPPTRAJ for 4 N-H vectors:
> >
> > trajin 1IEE_A_test.mdcrd
> > vector v0 .25 ired @26
> > vector v1 .41 ired @42
> > vector v2 .61 ired @62
> > vector v3 .68 ired @69
> > matrix ired name matired order 2
> > ###Attention: adjust vecs to number of residues in your protein
> > diagmatrix matired out ired.vec name ired.vec vecs 4
> > ired relax freq 500.0 NHdist 1.02 tstep 1.0 tcorr 10000.0 norm out v0
> > noefile noe \
> > order 2 modes ired.vec orderparamfile orderparam
> >
> > You will of course have to adjust parameters (such as vecs, tcorr, tstep,
> > freq etc) to fit your particular system.
> >
> > Hope this helps.
> >
> > -Dan
> >
> >
> >
> > On Wed, Dec 11, 2013 at 3:51 PM, 肖立 <xiaoli19871216.gmail.com> wrote:
> >
> > > Hi, all:
> > > I use the comment
> > > trajin ***.mdcrd
> > > vector ired_vector :1-468 ired 1:468 out ired_vector.dat
> > >
> > > to generate an ired vector.
> > > The program shows it can read the program and run it smoothly. However,
> > > there is no output file.
> > > I'm wondering if anyone knows what is wrong and how to generate an ired
> > > vector correctly.
> > >
> > > Best,
> > > Li
> > > --
> > > Li Xiao
> > > University of California, Irvine
> > > Email: xiaoli19871216.gmail.com
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > -------------------------
> > Daniel R. Roe, PhD
> > Department of Medicinal Chemistry
> > University of Utah
> > 30 South 2000 East, Room 201
> > Salt Lake City, UT 84112-5820
> > http://home.chpc.utah.edu/~cheatham/
> > (801) 587-9652
> > (801) 585-6208 (Fax)
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Li Xiao
> University of California, Irvine
> Email: xiaoli19871216.gmail.com
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>



-- 
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Wed Dec 11 2013 - 20:00:03 PST
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