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

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Wed, 11 Dec 2013 21:07:42 -0700

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)
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Received on Wed Dec 11 2013 - 20:30:03 PST
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