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
--
gmx-users mailing list
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
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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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
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
--
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
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)
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
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
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
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
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
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 finally del 1,
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
(save
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
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.
will be appreciate for any help.
Thanks for your help.
From: Justin A. Lemkul jalem...@vt.edu
To: Molecular Dynamics moleculardynam...@yahoo.com; Discussion list for
GROMACS users gmx-users@gromacs.org
Sent: Monday, October 3, 2011 5:17 PM
Subject: Re: [gmx-users] make_ndx
moleculardynam...@yahoo.com; Discussion list
for GROMACS users gmx-users@gromacs.org
*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
carbon-water using
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,
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
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
situation
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
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
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:
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
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
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
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
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
- Original Message -
From: Thomas Schlesier schl...@uni-mainz.de
Date: Friday, September 24, 2010 18:43
Subject: [gmx-users] make_ndx: execlude one group from another
To: gmx-users@gromacs.org gmx-users@gromacs.org
Hi all,
I'm trying to execlude all atoms of group 2 (140 atoms) from
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
1|12 merges the two groups into a new group
(112 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
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 112, 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 examples
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 112, which shows that the Group is empty
thanks in advance
Parthiban
___
gmx-users mailing listgmx-users@gromacs.org
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
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 anirban...@yahoo.co.in
Hi ALL,
I want to create an index file using make_ndx which will contain only
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
Hi,
Use splitat for group 3.
sharada
-- Original Message --
From: Venkat Reddy venkat...@gmail.com
To: Discussion list for GROMACS users gmx-users@gromacs.org
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
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
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.ndx
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
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
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
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, meant to
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 selcted
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
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
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
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.
___
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] wrote:
Hi All User
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 2007 20:08:06
To: 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 is a default group.
With regards
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
]
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,
Single out I mean
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 within
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
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 Life
From: Alan Dodd [EMAIL PROTECTED]
Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org
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
: [gmx-users] make_ndx and residue name length
From: Alan Dodd [EMAIL PROTECTED]
Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org
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
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
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
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, 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
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 accomplish
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
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
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
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