Olga Ivchenko wrote:
Dear Justin,
I ran you H bond frequency script and I got the following result. I am
understanding that the occupancy of H bonds is on the writeside, but
somehow in donor and acceptor column there is the residue name not atom
type. I am not quiet good iunderstanding my o
Dear Justin,
I ran you H bond frequency script and I got the following result. I am
understanding that the occupancy of H bonds is on the writeside, but somehow
in donor and acceptor column there is the residue name not atom type. I am
not quiet good iunderstanding my output. Please can you advice
Hi.
Did you inspect the contents of hbmap.xpm? There's a header followed by
matrix data. You can think of the matrix as ones and zeroes, represented
by the characters 'o' (= one) and ' ' (space = zero). As such, the rows
of the matrix are vecors containg ones and zeroes. Two such vectors can
Dear Justin,
Thank you very much.
best,
Olga
2010/11/29 Justin A. Lemkul
>
>
> Olga Ivchenko wrote:
>
>> Hi Leila,
>>
>> I am also have a task to calculate H-bonds frequency through the over all
>> trajectory in gromacs. Please can you send me Justin's script. If he does
>> not mind.
>>
>>
> I
Olga Ivchenko wrote:
Hi Leila,
I am also have a task to calculate H-bonds frequency through the over
all trajectory in gromacs. Please can you send me Justin's script. If he
does not mind.
I have several analysis scripts available to the public on my website:
http://www.bevanlab.biochem
Hi Leila,
I am also have a task to calculate H-bonds frequency through the over all
trajectory in gromacs. Please can you send me Justin's script. If he does
not mind.
Yours sincerely,
Olga
2010/11/29 leila karami
> Dear Mark and gromacs users
>
> thanks for your time and consideration.
>
> yo
Dear Mark and gromacs users
thanks for your time and consideration.
you said by multiplying the existence functions for hbonds between
protein and water and the hbonds between water
and DNA, then using Justin's script, I can obtain percentage each
water medited hydrogen bond during trajectory.
an
leila karami skrev 2010-11-25 11.37:
Dear Erik
thanks for your time and consideration.
you said by multiplying the existence functions for hbonds between
protein and water and the hbonds between water and DNA, then using
Justin's script, I can obtain percentage each water medited hydrogen
b
Dear Erik
thanks for your time and consideration.
you said by multiplying the existence functions for hbonds between protein
and water and the hbonds between water and DNA, then using Justin's script,
I can obtain percentage each water medited hydrogen bond during trajectory.
and also you said I
Well, yes. The 'h' notation is never used in the xpm file. I just
borrowed it from Luzar and chandler. Every line in the xpm data is the
h(t) for a particular hydrogen bond.
Erik
leila karami skrev 2010-11-24 16.50:
Dear Erik
I'm confused. is there h(t) in hbmap.xpm file?
where is h(t)? whi
Dear Erik
I'm confused. is there h(t) in hbmap.xpm file?
where is h(t)? which output file of g_hbond tool?
--
Leila Karami
Ph.D. student of Physical Chemistry
K.N. Toosi University of Technology
Theoretical Physical Chemistry Group
--
gmx-users mailing listgmx-users@gromacs.org
http://lis
Hi,
The -ins option is badly broken as far as I know. Don't expect it to
work anytime soon.
The hbmap.xpm depicts the existence functions h for all hydrogen bonds
as functuions of time. A red pixel means that the hydrogen bond is there
(h=1), white means that the hbond is broken (h=0). If yo
Dear Erik and Justin
Thank you so much for ypur help.
yes I mean water mediated hydrogen bonds (protein-H2O-dna).
since I'm beginner in perl script, please clarify your answer and explain
more. what is your mean of
existence functions exactly?
do using of -ins option in g_hbond tool help me?
Hi,
If you mean interactions bridged by a watermolecule, Protein-H2O-DNA,
then I don't know of any gromacs related tools for this. You need to
write your own tool for this. One way would be to multiply the existence
functions for hbonds between protein and water and the hbonds between
water a
Dear Justin
thanks for your attention
with chang of hbond.ndx file my problem was solved.
I have another question about g_hbond: if I want to obtain same information
(percentage of existence of each hbond during my trajectory) about water
mediated hydrogen bonds between protein and dna, for obta
Quoting leila karami :
> Dear Justin
>
> Thank you so much for help.
>
> I used # symbol in where you said and problem was solved. a output was
> obtained with name summary_HBmap.dat.
> this file is as follows:
>
> #DonorAcceptor% Exist.
>
Dear Justin
Thank you so much for help.
I used # symbol in where you said and problem was solved. a output was
obtained with name summary_HBmap.dat.
this file is as follows:
#DonorAcceptor% Exist.
Quoting leila karami :
> Dear Justin
>
> thank you very much.
>
> what I used as HB.pl exactly is as follows:
>
> is there problem in that?
>
> #!/usr/bin/perl
> #
> # plot_hbmap.pl - plot the probability of finding a particular hydrogen bond
> # based on several input files:
> # 1. coordinate f
Dear Justin
thank you very much.
what I used as HB.pl exactly is as follows:
is there problem in that?
#!/usr/bin/perl
#
# plot_hbmap.pl - plot the probability of finding a particular hydrogen bond
# based on several input files:
# 1. coordinate file (for atom naming) - MUST be a .pdb file wi
Quoting leila karami :
> Dear Justin
>
> when I use perl HB.pl -s .pdb -map .xpm -index .ndx, I encountered with:
>
> syntax error at ./HB.pl line 10, near "nothing else"
> "use" not allowed in expression at ./HB.pl line 13, at end of line
> Execution of ./HB.pl aborted due to compilation errors.
Dear Justin
when I use perl HB.pl -s .pdb -map .xpm -index .ndx, I encountered with:
syntax error at ./HB.pl line 10, near "nothing else"
"use" not allowed in expression at ./HB.pl line 13, at end of line
Execution of ./HB.pl aborted due to compilation errors.
--
Leila Karami
Ph.D. student of
Quoting leila karami :
> Dear Justin
>
> thanks for your time and attention
>
> yes of cource, I copy and paste correctly entire script from (first line) #
> ! /usr/bin/perl to (last line) exit. what is your mean of [There should be
> more information in the output if the program fails]? which out
Dear Justin
thanks for your time and attention
yes of cource, I copy and paste correctly entire script from (first line) #
! /usr/bin/perl to (last line) exit. what is your mean of [There should be
more information in the output if the program fails]? which output?
--
gmx-users mailing listg
Quoting leila karami :
> Dear Justin
>
> I study simulation of pr-dna complex. I want to know the percentage of
> existence of each hbond during my trajectory.
> I searched in previous lists. I want to use Perl script you offered to carla
> jamous:
> http://lists.gromacs.org/pipermail/gmx-users/20
Dear Carla
thanks for your attention
I used : perl HB.pl -s .pdb -map .xpm -index .ndx, but problem is there yet.
--
Leila Karami
Ph.D. student of Physical Chemistry
K.N. Toosi University of Technology
Theoretical Physical Chemistry Group
--
gmx-users mailing listgmx-users@gromacs.org
htt
Hi,
you should probably do:
perl HB.pl -s .pdb -map .xpm -index .xpm
More details are written inside the perl script.
Cheers,
Carla
On Tue, Nov 23, 2010 at 4:32 PM, leila karami wrote:
> Dear Justin
>
> I study simulation of pr-dna complex. I want to know the percentage of
> existence of each
Dear Justin
I study simulation of pr-dna complex. I want to know the percentage of
existence of each hbond during my trajectory.
I searched in previous lists. I want to use Perl script you offered to carla
jamous:
http://lists.gromacs.org/pipermail/gmx-users/2010-October/054727.html
I'm biginner
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