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

From: <wmsmith.uci.edu>
Date: Wed, 11 Dec 2013 16:45:28 -0800

Hi, Li:
 If the 500 residues fall in a nice simple numeric range, e.g. 1 to 500
then you could use a programing / scripting language of choice and a for
loop to print the needed commands to a ptraj script.

e.g. you could use a python script like:

f = open('ptraj.in','w')
for v in xrange(1,5):
        f.write('vector v%d :%d.N ired :%d.H\n' % (v,v,v))
f.close

which would produce:

vector v1 :1.N ired :1.H
vector v2 :2.N ired :2.H
vector v3 :3.N ired :3.H
vector v4 :4.N ired :4.H

in a file called ptraj.in

in your case, you would use xrange(1,501) to get numbers from 1 to 500.
If your residues are split into multiple non continuous ranges, you could
use separate for loops for each range.

Alternatively, you could do this same thing in VMD using the tcl scripting
language. That would give you access to the atomselect routines if your
need to set up some kind of special residue selection.
-Wes

> 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?
> 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, ‚–‹ <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
>
>



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Received on Wed Dec 11 2013 - 17:00:02 PST
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