On Tue, May 1, 2012 at 9:55 PM, Justin A. Lemkul wrote:
> On 5/1/12 2:40 PM, Lara Bunte wrote:
>> g_select -s molecule.pdb -select '"Close to ISO" resname SOL and within
>> 1.2 of resname ISO'
>>
>> and
>>
>> trjconv -n index.ndx -f molecule.pdb -s molecule.pdb -o output.pdb
>>
>> I got only water
On 5/1/12 4:12 PM, Lara Bunte wrote:
Hi Justin
Thanks, that makes sense. I have the group "Close to ISO" that contains the
water molecules in my specified region and I have the group ISO and therefore the next
step is to unite this two groups.
If I typed
make_ndx -f molecule.pdb -n inde
h "Close to ISO"?
Greetings
Lara
- Ursprüngliche Message -
Von: Justin A. Lemkul
An: Discussion list for GROMACS users
CC:
Gesendet: 20:55 Dienstag, 1.Mai 2012
Betreff: Re: [gmx-users] File editing - only one layer of water around a
molecule
On 5/1/12 2:40 PM, L
On 5/1/12 2:40 PM, Lara Bunte wrote:
Hi
There is a new problem :-(
If I used the commands
g_select -s molecule.pdb -select '"Close to ISO" resname SOL and within 1.2 of
resname ISO'
and
trjconv -n index.ndx -f molecule.pdb -s molecule.pdb -o output.pdb
I got only water in my output.pdb
Hi
There is a new problem :-(
If I used the commands
g_select -s molecule.pdb -select '"Close to ISO" resname SOL and within 1.2 of
resname ISO'
and
trjconv -n index.ndx -f molecule.pdb -s molecule.pdb -o output.pdb
I got only water in my output.pdb
Than I tried all 8 possible permutations
Hello
After I understand how to select a
molecule with water layers out of a molecule in a box filled with water
(again thanks to Justin and Mark for lots of help), I want to
understand more about choosing good parameters in g_select.
I have the command
g_select -s molecule_in_water.pdb -
or being such patient with me.
Greetings
Lara
- Ursprüngliche Message -
Von: Justin A. Lemkul
An: Discussion list for GROMACS users
CC:
Gesendet: 18:35 Montag, 30.April 2012
Betreff: Re: [gmx-users] File editing - only one layer of water around a
molecule
On 4/30/12 12:29 PM, Lara Bunte wrote
On 4/30/12 12:29 PM, Lara Bunte wrote:
Hi Justin
I got the error
Can not open file:
topol.tpr
if I type trjconv -n index.ndx -f molecule.pdb -o output.pdb -s
and I got the error
Can not open file:
traj.xtc
if I type trjconv -n index.ndx -f -s molecule.pdb -o output.pdb
What is the pr
helping me.
Lara
- Ursprüngliche Message -
Von: Justin A. Lemkul
An: Lara Bunte ; Discussion list for GROMACS users
CC:
Gesendet: 18:07 Montag, 30.April 2012
Betreff: Re: [gmx-users] File editing - only one layer of water around a
molecule
On 4/30/12 11:41 AM, Lara Bunte wrote
On 4/30/12 11:41 AM, Lara Bunte wrote:
Hi
I have the command
trjconv -n index.ndx -f molecule.pdb -o output.pdb
that don't work because of the missing topol.tpr file. You wrote:
Supply your .pdb file to the -s flag
Where exactly do I have to write -s in my command?
Anywhere. Order
üngliche Message -
Von: Justin A. Lemkul
An: Discussion list for GROMACS users
CC:
Gesendet: 19:44 Montag, 23.April 2012
Betreff: Re: [gmx-users] File editing - only one layer of water around a
molecule
On 4/23/12 1:27 PM, Lara Bunte wrote:
> Hi
>
> In this case my problem is
On 4/23/12 1:27 PM, Lara Bunte wrote:
Hi
In this case my problem is not solvable with gromacs?
All I have is the my_molecule.pdb which is a small molecule in a water box and
my generated index.ndx file, size.xvg file and output.xtc file.
Supply your .pdb file to the -s flag. Sorry for my
; Discussion list for GROMACS users
CC:
Gesendet: 19:20 Montag, 23.April 2012
Betreff: Re: [gmx-users] File editing - only one layer of water around a
molecule
On 4/23/12 1:13 PM, Lara Bunte wrote:
> Hi
> If I use
>
> trjconv -n index.ndx -f my_molecule.pdb -o output.pdb
>
>
On 4/23/12 1:13 PM, Lara Bunte wrote:
Hi
If I use
trjconv -n index.ndx -f my_molecule.pdb -o output.pdb
I got this error again
Can not open file:
topol.tpr
Whats now the problem?
Apparently you need a .tpr file supplied to the -s flag to do such a
transformation. I'm not sure why it's
.April 2012
Betreff: Re: [gmx-users] File editing - only one layer of water around a
molecule
On 4/23/12 11:01 AM, Lara Bunte wrote:
> Hi
>
> What do you mean with
>
>
>> Specify a .pdb file as the output of your original command.
>
> I wrote in
>
>
> tr
On 4/23/12 11:01 AM, Lara Bunte wrote:
Hi
What do you mean with
Specify a .pdb file as the output of your original command.
I wrote in
trjconv -s -f output.xtc -o output.pdb
in the last part output.pdb. What should I specify more?
When I was referring to your "original command," I
An: Discussion list for GROMACS users
CC:
Gesendet: 13:02 Montag, 23.April 2012
Betreff: Re: [gmx-users] File editing - only one layer of water around a
molecule
On 4/23/12 3:46 AM, Lara Bunte wrote:
>
>
> Hi
>
> that worked. I used
>
> trjconv -n index.ndx -f my_molecule.pdb -o o
On 4/23/12 3:46 AM, Lara Bunte wrote:
Hi
that worked. I used
trjconv -n index.ndx -f my_molecule.pdb -o output
After this I got an trajectory file output.xtc
Now I have to get really a coordinate file, i.e. pdb file. I used the command
trjconv -s -f output.xtc -o output.pdb
to convert
l
An: Discussion list for GROMACS users
Gesendet: 23:10 Sonntag, 22.April 2012
Betreff: Re: [gmx-users] File editing - only one layer of water around a
molecule
On 4/22/12 5:07 PM, Lara Bunte wrote:
> Hi
>
> I got always the same error. I tried
>
> trjconv -n index.ndx -s molecule_in
On 4/22/12 5:07 PM, Lara Bunte wrote:
Hi
I got always the same error. I tried
trjconv -n index.ndx -s molecule_in_water.pdb -o output
Could you please send an example command how to get the coordinate file out of
my index file?
I typed trjconv -h but I can't filter the knowledge out, thats
s for helping
Greetings
Lara
Von: Justin A. Lemkul
An: Discussion list for GROMACS users
Gesendet: 22:37 Sonntag, 22.April 2012
Betreff: Re: [gmx-users] File editing - only one layer of water around a
molecule
On 4/22/12 3:55 PM, Lara Bunte wrote:
> H
On 4/22/12 3:55 PM, Lara Bunte wrote:
Hi Justin
You wrote:
>If you do not specify any output file, the default is this .xvg file that
tells you how many atoms satisfied the >criterion specified in the selection
string. If you want a coordinate file, it's a two-step process.
>
>1. Run g_sel
__
Von: Justin A. Lemkul
An: Discussion list for GROMACS users
Gesendet: 17:27 Samstag, 14.April 2012
Betreff: Re: [gmx-users] File editing - only one layer of water around a
molecule
Lara Bunte wrote:
> Hi Justin
>
> The difference in my
>
> g_select
ere someone using yahoo also
and know how to fix this?
--------
*Von:* Justin A. Lemkul
*An:* Lara Bunte ; Discussion list for GROMACS
users
*Gesendet:* 16:56 Samstag, 14.April 2012
*Betreff:* Re: [gmx-users] File editing - on
thing like
that. Again after pressing answer the mail should go only to Justin. I
put the mailing list in cc. Is here someone using yahoo also and know
how to fix this?
----------------
*Von:* Justin A. Lemkul
*An:* Lara Bunte ; Discussion list for GROMACS
users
*Gesendet:* 16:56 Sams
Von: Justin A. Lemkul
An: Lara Bunte ; Discussion list for GROMACS users
Gesendet: 16:56 Samstag, 14.April 2012
Betreff: Re: [gmx-users] File editing - only one layer of water around a
molecule
Lara Bunte wrote:
> I still got the problem. What is wrong in this command:
>
> g_
Lara Bunte wrote:
I still got the problem. What is wrong in this command:
g_select -s molecule_in_water.pdb -select '"Close to ISO" resname SOL
and within 0.5 of group "ISO"'
In the pdb. file ISO is for the molecule and SOL for the water.
Please help
The above command assumes "ISO" is a
Please help
Greetings
Lara
Von: Teemu Murtola
An: Discussion list for GROMACS users
Gesendet: 18:20 Freitag, 13.April 2012
Betreff: Re: [gmx-users] File editing - only one layer of water around a
molecule
On Fri, Apr 13, 2012 at 18:30, Lara Bunte wrote:
> Is there no way only to use the
On Fri, Apr 13, 2012 at 18:30, Lara Bunte wrote:
> Is there no way only to use the .pdb file? How do I create from a .pdb a rtp
> file. With pdb2gmx and than grompp?
You can also provide a .pdb file to the -s option of g_select. And you
don't need to provide a -f file in that case if you simply w
Lara Bunte wrote:
Hi
You are totally right. I am sorry. It is just so frustrating if you read
the complete help more than once, understand nothing and than here all
the time, that I should read the help. :-(
I like Gromacs and I am happy that it is free and I am very thankful for
all the
ply-all by default or replace the address.
-Justin
>
>
>
> --------------------
> *Von:* Justin A. Lemkul
> *An:* Lara Bunte ; Discussion list for GROMACS users
>
> *Gesendet:* 14:59 Freitag, 13.April 2012
> *Betre
MACS
users
*Gesendet:* 14:59 Freitag, 13.April 2012
*Betreff:* Re: [gmx-users] File editing - only one layer of water around
a molecule
Lara Bunte wrote:
> Hi
>
> I tried but I got an error. In my mol_in_water.pdb file all atoms of
my molecule has the group notation ISO and all
endet: 14:59 Freitag, 13.April 2012
Betreff: Re: [gmx-users] File editing - only one layer of water around a
molecule
Lara Bunte wrote:
> Hi
>
> I tried but I got an error. In my mol_in_water.pdb file all atoms of my
> molecule has the group notation ISO and all the water atoms
Lara Bunte wrote:
Hi
I tried but I got an error. In my mol_in_water.pdb file all atoms of my
molecule has the group notation ISO and all the water atoms has the
group notation SOL. I used following command:
g_select -f my mol_in_water.pdb -other -options -select '"Close to ISO"
resname SO
the kind of
usage "general knowledge" that can often be acquired that way.
Mark
>
>Greetings
>Lara
>
>
>
>
>
>
>
> Von: Mark Abraham
>An: Discussion list for GROMACS users
>Gesendet: 12:06 Freitag, 13.April
rk
Greetings
Lara
*Von:* Mark Abraham
*An:* Discussion list for GROMACS users
*Gesendet:* 12:06 Freitag, 13.April 2012
*Betreff:* Re: [gmx-users] File editing - only one layer of water
around a molecule
On 13/04/201
Betreff: Re: [gmx-users] File editing - only one layer of water around a
molecule
On 13/04/2012 8:01 PM, Lara Bunte wrote:
Hi Mark
>
>
>Could you please give me for that the prompt how to write this in the console.
>
>
>
>"All atoms of a residue LIG within 0.5 nm o
ully the use of single and double quotes.
Mark
Greetings
Lara
*Von:* Mark Abraham
*An:* Discussion list for GROMACS users
*Gesendet:* 11:51 Freitag, 13.April 2012
*Betreff:* Re: [gmx-users] File editing - only one layer of water
around a molecule
On 13/04/2012 7:29 PM, Lara Bunte wrote
Gesendet: 11:51 Freitag, 13.April 2012
Betreff: Re: [gmx-users] File editing - only one layer of water around a
molecule
On 13/04/2012 7:29 PM, Lara Bunte wrote:
I read g_select -select 'help all' and I understand nothing of that.
>
>
>
>In general one have a molecule (vale
ham
*An:* Discussion list for GROMACS users
*Gesendet:* 19:26 Mittwoch, 11.April 2012
*Betreff:* Re: [gmx-users] File editing - only one layer of water
around a molecule
On 12/04/2012 3:24 AM, Justin A. Lemkul wrote:
>
>
> Lara Bunte wrote:
>> Could you please give how g_select is
to do this with gromacs. I read the
>> examples in g_select -select 'help all' and I have no Idea what they are
>> talking about.
>>
>> Thanks for help
>> Greetings
>> Lara
>>
>>
>>
>> --
>>
-
> *Von:* Mark Abraham
> *An:* Discussion list for GROMACS users
> *Gesendet:* 19:26 Mittwoch, 11.April 2012
>
> *Betreff:* Re: [gmx-users] File editing - only one layer of water around
> a molecule
>
> On 12/04/2012 3:24 AM, Justin A. Lemkul wrote:
> >
>
Re: [gmx-users] File editing - only one layer of water around a
molecule
On 12/04/2012 3:24 AM, Justin A. Lemkul wrote:
>
>
> Lara Bunte wrote:
>> Could you please give how g_select is used?
Reading g_select -h might have led you to try g_select -select 'help'
>&
On 12/04/2012 3:24 AM, Justin A. Lemkul wrote:
Lara Bunte wrote:
Could you please give how g_select is used?
Reading g_select -h might have led you to try g_select -select 'help'
Is there a tutorial for that?
g_select -select 'help all'
The information contained therein is very extensi
Lara Bunte wrote:
Could you please give how g_select is used?
Is there a tutorial for that?
g_select -select 'help all'
The information contained therein is very extensive, so be sure to read it
thoroughly. It will fill several terminal windows explaining the syntax and
providing example
____
> Von: Mark Abraham
>An: Lara Bunte
>Gesendet: 14:07 Mittwoch, 11.April 2012
>Betreff: Re: [gmx-users] File editing - only one layer of water around a
>molecule
>
>
>
> On 11/04/12, Lara Bunte wrote:
>Hi
>>
>>I read g_select d
en atoms, which is all that
you have to work with.
Mark
Greetings
Lara
- Ursprüngliche Message -
Von: Mark Abraham
An: Discussion list for GROMACS users
CC:
Gesendet: 14:27 Mittwoch, 4.April 2012
Betreff: Re: [gmx-users] File editing - only one layer of water
around a molecule
Lara
- Ursprüngliche Message -
Von: Mark Abraham
An: Discussion list for GROMACS users
CC:
Gesendet: 14:27 Mittwoch, 4.April 2012
Betreff: Re: [gmx-users] File editing - only one layer of water around a
molecule
On 4/04/2012 7:27 PM, Lara Bunte wrote:
> Hello
>
> I h
On 4/04/2012 7:27 PM, Lara Bunte wrote:
Hello
I have a question about editing a pdb file.
I have a molecule in a box of water as a pdb file. I want to remove all water
except of ONE layer around he molecule. How to do that?
Do you know a software that is able to do that? Do you know how it
Hello
I have a question about editing a pdb file.
I have a molecule in a box of water as a pdb file. I want to remove all water
except of ONE layer around he molecule. How to do that?
Do you know a software that is able to do that? Do you know how it could work
with programs like PyMol or o
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