On 1/26/13 1:57 PM, Albert wrote:
On 01/26/2013 07:51 PM, Justin Lemkul wrote:
Can you please post the following:
1. The groups printed in the make_ndx prompt
2. The output of gmxcheck on an index file created from your coordinate file
(created simply by typing 'q' at the prompt, i.e. not cr
On 01/26/2013 07:51 PM, Justin Lemkul wrote:
Can you please post the following:
1. The groups printed in the make_ndx prompt
2. The output of gmxcheck on an index file created from your
coordinate file (created simply by typing 'q' at the prompt, i.e. not
creating any special groups)
-Justi
On 1/26/13 1:49 PM, Albert wrote:
On 01/26/2013 07:41 PM, Justin Lemkul wrote:
What types of ions do you have? I can reproduce this problem for a protein
with ions bound to it, which are numbered discontinuously with water and ions
in solution.
-Justin
thank you for kind reply.
I only ha
On 01/26/2013 07:41 PM, Justin Lemkul wrote:
What types of ions do you have? I can reproduce this problem for a
protein with ions bound to it, which are numbered discontinuously with
water and ions in solution.
-Justin
thank you for kind reply.
I only have Na+ and Cl-.
best
Albert
--
gm
On 1/26/13 1:30 PM, Albert wrote:
On 01/26/2013 06:53 PM, Justin Lemkul wrote:
What exactly did you enter at the make_ndx prompt?
-Justin
1|25
protein, water and ions
What types of ions do you have? I can reproduce this problem for a protein with
ions bound to it, which are numb
On 01/26/2013 06:53 PM, Justin Lemkul wrote:
What exactly did you enter at the make_ndx prompt?
-Justin
1|25
protein, water and ions
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* Please search the archive at
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On 1/26/13 12:25 PM, Albert wrote:
Hello:
I am using make_ndx to make a index file in Gromacs 4.6,
make_ndx -f input.pdb
but it said:
Copied index group 1 'Protein'
Copied index group 25 'Water_and_ions'
One of your groups is not ascending
Group is empty
What exactly did you enter a
Hello:
I am using make_ndx to make a index file in Gromacs 4.6,
make_ndx -f input.pdb
but it said:
Copied index group 1 'Protein'
Copied index group 25 'Water_and_ions'
One of your groups is not ascending
Group is empty
thank you very much
best
Albert
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gmx-users mailing listgmx-users
On 9/29/12 3:02 PM, Ali Alizadeh wrote:
Dear All users
make_ndx
How to i can create a my especial index file?
Is there a tutorial related to it?
http://www.gromacs.org/Documentation/Gromacs_Utilities/make_ndx
Also, typing "help" at the prompt when running make_ndx provides examples and
On 7/31/12 10:14 AM, Laura Kingsley wrote:
Hello,
I've just switched from using Gromacs version 4.0.5 to 4.5.5, and I'm having an
issue with make_ndx. Using the old version I have a single group showing up for
each "odd" residue, eg JJJ shows up once as group 16 for example. When I use the
new
Hello,
I've just switched from using Gromacs version 4.0.5 to 4.5.5, and I'm
having an issue with make_ndx. Using the old version I have a single
group showing up for each "odd" residue, eg JJJ shows up once as group
16 for example. When I use the new version on the same file I get 2
groups a
Hi all
I'd like to do a selection of atom names such as:
a C1 C3 C2 C4
to get an index file with 4 atoms (no other matches in the file) and
then use it with g_angle to calculate the dihedral. The problem is that
make_ndx does not keep the order of atoms in the resulting index file as
they ar
On 1/02/2012 5:02 AM, Zhuyi Xue wrote:
Hi, there
I would like to select, for example, CA of GLY, CB of PRO, so I typed r
GLY& a CA | r PRO& a CB, but it doesn't work. make_ndx also doesn't
support parenthesis, either.
Previously, I used "r GLY& a CA" (save as group 1), then "r PRO& a CB"
Hi, there
I would like to select, for example, CA of GLY, CB of PRO, so I typed r
GLY& a CA | r PRO& a CB, but it doesn't work. make_ndx also doesn't
support parenthesis, either.
Previously, I used "r GLY& a CA" (save as group 1), then "r PRO& a CB"
(save as group 2), then "1|2", and final
--
*From:* Justin A. Lemkul
*To:* Molecular Dynamics ; Discussion list
for GROMACS users
*Sent:* Monday, October 3, 2011 5:17 PM
*Subject:* Re: [gmx-users] make_ndx and rdf
Molecular Dynamics wrote:
> Dear All,
>
> I want to calculate rdf for carbon-oxygen, carbon-hydrogen and
car
g list. So I will be appreciate for any help.
Thanks for your help.
From: Justin A. Lemkul
To: Molecular Dynamics ; Discussion list for
GROMACS users
Sent: Monday, October 3, 2011 5:17 PM
Subject: Re: [gmx-users] make_ndx and rdf
Molecular Dynamics wrote:
>
Molecular Dynamics wrote:
Dear All,
I want to calculate rdf for carbon-oxygen, carbon-hydrogen and
carbon-water using g_rdf but how can I generate an .ndx file that are
suitable for these systems ? I searched mailing list and read manual but
couldn't generate .ndx file using make_ndx tool.
Dear All,
I want to calculate rdf for carbon-oxygen, carbon-hydrogen and carbon-water
using g_rdf but how can I generate an .ndx file that are suitable for these
systems ? I searched mailing list and read manual but couldn't generate .ndx
file using make_ndx tool. However, I tried to see the ma
ram bio wrote:
Dear Gromacs Users,
I have simulated a protein -ligand complex in the popc bilayer and while
analysing the results i want to find distance between two residues in
the protein during simulation. For that I think I have to use g_hbond
command by creating an index.file containi
Dear Gromacs Users,
I have simulated a protein -ligand complex in the popc bilayer and while
analysing the results i want to find distance between two residues in the
protein during simulation. For that I think I have to use g_hbond command
by creating an index.file containing the new groups, but
Hi,
Does the "!" in make_ndx work?
"|" and "&" work, but seems "!" not work.
I met something weird,
suppose
I choose a C11, which is from ri 1-111.
if use
a C11, the atom is 111
if use
a C11 & ri 1-111, the atom is 111
if use
a C11 & ri 101-111, the atom is 5. Which is expected to be 10, so this
Paymon Pirzadeh wrote:
I assumption was that when provide the index file, do_dssp will do the
analysis for the protein but prints out the results only for the
designated residues. All I wanted was a better resolution on the final
When prompted for only one group, that group is used for calcul
I assumption was that when provide the index file, do_dssp will do the
analysis for the protein but prints out the results only for the
designated residues. All I wanted was a better resolution on the final
xpm plot to see the secondary structure of the protein at those residues
of interest. Any su
Paymon Pirzadeh wrote:
Justin,
I produced the index file based on your suggestion, but when I ran the
do_dssp, a completely different result was spit out comparing to what
the whole protein analysis had given. Any ideas on why that might have
happened?
That depends on what "completely differ
Justin,
I produced the index file based on your suggestion, but when I ran the
do_dssp, a completely different result was spit out comparing to what
the whole protein analysis had given. Any ideas on why that might have
happened?
Paymon
On Wed, 2010-10-06 at 14:42 -0400, Justin A. Lemkul wrote:
>
Paymon Pirzadeh wrote:
Hello, I want to check the secondary structure of protein at particular
residues. Since dssp needs all main chain atoms, does the following command
at the make_ndx prompt makes the correct index file?
You can answer that yourself by looking at the resulting index file.
Hello,
I want to check the secondary structure of protein at particular residues.
Since dssp needs all main chain atoms, does the following command at the
make_ndx prompt makes the correct index file?
5 | r 1 | r 10-11 |r 14-17 | r 20-21 | r 26-32 | r 42 | r 45
(Main chain atom of particular
Hi all,
I'm trying to execlude all atoms of group 2 (140 atoms) from group 1
(300 atoms), so that i have a new group 3 (with 160 atoms).
| is for merging with OR
& for merging with AND
so ! should be for merging with NOT
But i tried
1 ! 2
2 ! 1
but in both cases make_ndx complains about syntax e
- Original Message -
From: Thomas Schlesier
Date: Friday, September 24, 2010 18:43
Subject: [gmx-users] make_ndx: execlude one group from another
To: "gmx-users@gromacs.org"
> Hi all,
> I'm trying to execlude all atoms of group 2 (140 atoms) from
> group 1 (30
Thomas Schlesier skrev 2010-09-23 13.03:
Hi all,
I'm trying to execlude all atoms of group 2 (140 atoms) from group 1
(300 atoms), so that i have a new group 3 (with 160 atoms).
| is for merging with OR
& for merging with AND
so ! should be for merging with NOT
But i tried
1 ! 2
2 ! 1
but in b
Hi all,
I'm trying to execlude all atoms of group 2 (140 atoms) from group 1
(300 atoms), so that i have a new group 3 (with 160 atoms).
| is for merging with OR
& for merging with AND
so ! should be for merging with NOT
But i tried
1 ! 2
2 ! 1
but in both cases make_ndx complains about syntax e
parthi...@ncbs.res.in wrote:
Hi
Anyone can please tell how to index 2 or more groups using make_ndx
eg: 1 protein
12 sol
13 NA+
i tried giving >1&12, which shows that the "Group is empty"
Type "help" at the make_ndx prompt; you will see a number of examples.
There are also more exa
1|12 merges the two groups into a new group
(1&12 will merge into a new group any atoms which are in both groups 1 and
12, of which there are none in this case)
Tom
--On Wednesday, August 26, 2009 04:07:20 +0530 parthi...@ncbs.res.in wrote:
Hi
Anyone can please tell how to index 2 or more
Hi
Anyone can please tell how to index 2 or more groups using make_ndx
eg: 1 protein
12 sol
13 NA+
i tried giving >1&12, which shows that the "Group is empty"
thanks in advance
Parthiban
___
gmx-users mailing listgmx-users@gromacs.org
http
Hi,
Use splitat for group 3.
sharada
-- Original Message --
From: Venkat Reddy
To: Discussion list for GROMACS users
Date: Thu, 9 Jul 2009 19:54:18 +0530
Subject: Re: [gmx-users] make_ndx option
Hi Anirban !
First u hav to notedown the C-alpha atoms nos seperately from ur atom file.
Then
Hi Anirban !
First u hav to notedown the C-alpha atoms nos seperately from ur atom file.
Then execute the command "make_ndx -f input.gro -o index.ndx".After this
command, it gives a prompt. At that prompt you have to make a new group for
the core region, for this you need to have the list of resid
Hi Anirban,
when you choose in make_ndx, you choose group 3 and (&) r 2 3 4 5 6...and so
on...
in make_ndx there is a legend that explain this passage well...
Bye!
2009/7/9 Anirban Ghosh
> Hi ALL,
>
> I want to create an index file using make_ndx which will contain only
> C-alpha atoms of some r
Hi ALL,
I want to create an index file using make_ndx which will contain only C-alpha
atoms of some residues (like from residue no 2-10, res 25-30, res 36-40). How
should I give this option in make_ndx. Any suggestion is welcome.
Regards,
Anirban GhoshGrade Based Engineer
Bioinformatics Team
I'm having trouble with using make_ndx with a specific file. Whenever I try to
combine or use a specific group (group content at bottom) I get the error "One
of your groups is not ascending", and the group is not actually included in the
subsequent group produced. As far as I can see, the numb
I think, after creating an index file, you can edit it manually clubbing both
Phosphorius and Oxygen atoms together ( considering as a single group). Then
specify this group while doing analysis.
On Wed, 16 Jul 2008 minnale wrote :
> Thanks for the reply, may be this is trivial question to
Thanks once again.
Ideally I shouldnt do for whole system.
Ok.
On Wed, 16 Jul 2008 Justin A.Lemkul wrote :
>
>
>minnale wrote:
>> but here I am calculating density for 128 lipids not for 64 lipids. Is it
>> right what iam doing?
>
>The examples on the wiki are just a few illustrative ideas, m
minnale wrote:
but here I am calculating density for 128 lipids not for 64 lipids. Is
it right what iam doing?
The examples on the wiki are just a few illustrative ideas, meant to inspire the
fact that you can analyze whatever subset of your system you wish. You can
certainly analyze all
minnale wrote:
Thanks for the reply, may be this is trivial question to you
That I know that how to select phosrous atom alone of POPC.
Normally people are using only phosphrous atom or PO4 group ? for
density calculation ,etc analysis. In one article I found that they have
done density ana
Thanks for the reply, may be this is trivial question to you
That I know that how to select phosrous atom alone of POPC.
Normally people are using only phosphrous atom or PO4 group ? for density
calculation ,etc analysis. In one article I found that they have done density
analysis for PO4 group
Hi,
On Wednesday, 16. July 2008, minnale wrote:
> Hi Users,
> I want to do analysis of g_density of lipidbilayer so how can I select po4
> and N(CH3)3 groups seperately by using make_ndx from popc. Can anyone tell
> me detail with which options use?
> I have checked in archives that create sn1.nd
minnale wrote:
Hi Users,
I want to do analysis of g_density of lipidbilayer so how can I select
po4 and N(CH3)3 groups seperately by using make_ndx from popc.
Can anyone tell me detail with which options use?
I have checked in archives that create sn1.ndx and sn2.ndx files but i
didnt get c
Hi Users,
I want to do analysis of g_density of lipidbilayer so how can I select po4 and
N(CH3)3 groups seperately by using make_ndx from popc.
Can anyone tell me detail with which options use?
I have checked in archives that create sn1.ndx and sn2.ndx files but i didnt
get celarly.
Thanks
On 7 May 2008 07:10:11 -
"minnale " <[EMAIL PROTECTED]> wrote:
Hi all,
it may be trivial question
My protien contain nearly 200 residues, I want plot RMSD for 45 to 90
residues , So I made make_ndx file also, but I am doubting that what i have I
done whether right ot wrong?
I have selct
Hi all,
it may be trivial question
My protien contain nearly 200 residues, I want plot RMSD for 45 to 90 residues
, So I made make_ndx file also, but I am doubting that what i have I done
whether right ot wrong?
I have selcted
1 | r 45-90 1 = protein , the way I have selected is correct or
Hi,
I want to create an index file which will contain indices of all the
atoms in two monolayers separately in a bilayer. For this purpose
I have copied a python script from a post in gromacs mailing list, and
did a simple modification. But after modification, make_ndx gives
me error like "Group 1
Thanks Mark,
I could do it following your suggestion.
Sarbani
On Wed, 24 Oct 2007 Mark Abraham wrote :
>sarbani chattopadhyay wrote:
>> hi,
>> I want to select two groups in the index
sarbani chattopadhyay wrote:
hi,
I want to select two groups in the index file, one group consisting
of only the aromatic
ring of phenylalanine and the other group consisting of only the alpha
carbon.
I want to know the way to use the make_ndx command for this.
After entering make_ndx
hi,
I want to select two groups in the index file, one group consisting of
only the aromatic
ring of phenylalanine and the other group consisting of only the alpha carbon.
I want to know the way to use the make_ndx command for this.
___
gmx-use
PROTECTED] on behalf of David van der Spoel
Sent: Thu 27/09/2007 7:29 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] make_ndx
Naser, Md Abu wrote:
> Thanks david!
>
oops I misread. Sidechains do not contain C-alpha (which you can easily
check in the index file).
So
]
Phone: +44(0)1314518265
Fax : +44(0) 131 451 3009
-Original Message-
From: [EMAIL PROTECTED] on behalf of David van der Spoel
Sent: Thu 27/09/2007 7:17 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] make_ndx
Naser, Md Abu wrote:
> Hi XAvier,
>
> "
egards,
Abu Naser
School Of Life Sciences
Heriot-Watt University
Edinburgh EH14 4AS
Email: [EMAIL PROTECTED]
Phone: +44(0)1314518265
Fax : +44(0) 131 451 3009
-Original Message-
From: [EMAIL PROTECTED] on behalf of Xavier Periole
Sent: Wed 26/09/2007 8:42 PM
To: Discussion
: Discussion list for GROMACS users
Subject: Re: [gmx-users] make_ndx
Naser, Md Abu wrote:
> Hi XAvier,
>
> "Single out" I mean pick up only the side chain bonded with alpha
> carbon atom and
> put them in a group using make_ndx.
>
all side chains are.
and sidechain
University
Edinburgh EH14 4AS
Email: [EMAIL PROTECTED]
Phone: +44(0)1314518265
Fax : +44(0) 131 451 3009
-Original Message-
From: [EMAIL PROTECTED] on behalf of Xavier Periole
Sent: Wed 26/09/2007 8:42 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] make_ndx
On Wed, 26 Sep
+44(0) 131 451 3009
-Original Message-
From: [EMAIL PROTECTED] on behalf of Xavier Periole
Sent: Wed 26/09/2007 8:42 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] make_ndx
On Wed, 26 Sep 2007 20:08:06 +0100
"Naser, Md Abu" <[EMAIL PROTECTED
On Wed, 26 Sep 2007 20:08:06 +0100
"Naser, Md Abu" <[EMAIL PROTECTED]> wrote:
Hi All User,
Is there anyway I can single out side chain of alpha carbon atom using
make_ndx?
What do you mean by "single out"
and with "side chain of alpha carbon" ?
Thanks in advance.
Abu Naser
School Of Li
Hi All User,
Is there anyway I can single out side chain of alpha carbon atom using make_ndx?
Thanks in advance.
Abu Naser
School Of Life Sciences
Heriot-Watt University
Edinburgh EH14 4AS
Email: [EMAIL PROTECTED]
Phone: +44(0)1314518265
Fax : +44(0) 131 451 3009
Subject: RE: [gmx-users] make_ndx and residue name length
>From: Alan Dodd <[EMAIL PROTECTED]>
>Reply-To: Discussion list for GROMACS users
>To: gmx-users@gromacs.org
>Subject: [gmx-users] make_ndx and residue name length
>Date: Tue, 4 Sep 2007 10:55:07 -0700 (PDT)
>
&g
From: Alan Dodd <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users
To: gmx-users@gromacs.org
Subject: [gmx-users] make_ndx and residue name length
Date: Tue, 4 Sep 2007 10:55:07 -0700 (PDT)
The maximum permissible residue name length is at least 5 characters long
for a
The maximum permissible residue name length is at least 5 characters long for a
tpr or gro, but the length of residue name permitted by make_ndx is only 4
characters. And of course, pdb should have only 3 characters. While I can
change the names in a gro or a pdb quite quickly and easily, is t
Camilo,
>What is missing here? Why does make_ndx not see the individual atoms
in the configuration file?
What is displayed by make_ndx when you have execute it?
Which particular file do you run it on?
Catch ya,
Dr. Dallas Warren
Lecturer
Department of Pharmaceutical Biology and Pharmacology
Hello all,
I am trying to generate an index file for a box of solvent, and I must be
missing a key detail somewhere...
The following is the command that I am using:
make_ndx -f conf.gro -o index.ndx
The conf.gro that I am using is the same as one of those provided in the
'top' folder, which is
Hello, Manuel,
Thank you very much for your trick. It is neat.
Have a nice weekend!
Dongsheng
On Sun, 2006-06-25 at 02:58 +0200, Manuel Prinz wrote:
> Hello Dongsheng!
>
> Am Samstag, den 24.06.2006, 17:26 -0400 schrieb Dongsheng Zhang:
> > In make_ndx, I would like to keep two groups, for in
Hello Dongsheng!
Am Samstag, den 24.06.2006, 17:26 -0400 schrieb Dongsheng Zhang:
> In make_ndx, I would like to keep two groups, for instance, group 4 and
> group 5. I have try it in two ways, namely, "keep 4 & keep 5" and "keep
> 4 | keep 5". However both ways only keep group 4. Anyway to accom
Hello, gmx users:
In make_ndx, I would like to keep two groups, for instance, group 4 and
group 5. I have try it in two ways, namely, "keep 4 & keep 5" and "keep
4 | keep 5". However both ways only keep group 4. Anyway to accomplish
my task is to delete other groups one by one, but it is not so
c
bharat v. adkar wrote:
Dear GMX users...
i have a protein-peptide complex wherein peptide does not have one of
the terminal carboxy oxygen atoms (i.e., it has -CO only). I designate A
to peptide and B to protein chain. when i do pdb2gmx, it adds the
missing O, so now the group is -COO. Now w
Dear GMX users...
i have a protein-peptide complex wherein peptide does not have one of the
terminal carboxy oxygen atoms (i.e., it has -CO only). I designate A to
peptide and B to protein chain. when i do pdb2gmx, it adds the missing O,
so now the group is -COO. Now with this gro file, i tri
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