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

From: 肖立 <xiaoli19871216.gmail.com>
Date: Wed, 11 Dec 2013 21:36:37 -0800

Thanks a lot!
Li


On Wed, Dec 11, 2013 at 8:07 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:

> One more thing - you should probably add '.N' to the mask as well so you
> don't pick up extraneous N's in e.g. ASN residues, something like:
>
> select .N&@%N&!:PRO
>
>
>
> On Wed, Dec 11, 2013 at 8:57 PM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
>
> > 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)
> >
>
>
>
> --
> -------------------------
> 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
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Received on Wed Dec 11 2013 - 22:00:02 PST
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