[gmx-users] gmx select

[Pandya, Akash]

Hi all,

I'm trying to work out how many molecules of ligand and water I have within a 
certain distance. I used the gmx select command below:

gmx select -f trajectory.gro -s trajectory.tpr -oi index.dat -select 'resname 
LIG and within 0.5 of whole_res_com of resnr 1' -dt 100

However, this only outputs atomic positions. How can I get the number of "whole 
molecules"? If that makes sense? Or is there another command I can use?

Akash

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[gmx-users] gmx select help

[Pandya, Akash]

Hi all,

I am running the gmx select command to create a file with all my ligand 
molecules that are within  the cut-off distance specified from the COM of a 
protein residue as a function of time. Here is the command I am using:


gmx select -f traj2.gro -s protein.tpr -dt 100 -on index.ndx -select 'resname 
LIG and within 0.5 of res_com of resnr 183' -resnr number


The file currently outputs atom numbers for my ligand molecules. If I only 
wanted the resid of my ligands (as named in the trajectory file, e.g. resid 130 
LIG) instead of the atom id  to be written, how would I do this?

Akash

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[gmx-users] gmx select

[Pandya, Akash]

Hi all,

I am running the gmx select command to obtain all my ligand molecules that are 
within a cut-off distance from the COM of a protein residue as a function of 
time. The output from the command below comes with just the atom positions of 
my ligand.


gmx select -f protein_gly.gro -s protein.tpr -n mindist1.ndx -dt 100 -oi 
index.dat -select 'resname LIG and within 3 of res_com of resnr 183' -resnr 
index


Is there a way to only output the residue number instead of the atom numbers?

Akash
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Re: [gmx-users] gmx select with coordinates

[Shan Jayasinghe]

Hi Prof. Dan,

Thank you very much  for the e-mail. How do we define coordinates what we
want in VMD Graphical Representation menu?

Thank you.

On Wed, Oct 10, 2018 at 6:53 AM Dan Gil  wrote:

> Hi Shan,
>
> Sorry it's been a while - I don't check this email too often. Did you
> figure the problem out?
>
> I use the Graphical Representations menu of VMD, although I am sure there
> is a way to do it in the console too.
>
> On Thu, Sep 27, 2018 at 9:35 PM Shan Jayasinghe <
> shanjayasinghe2...@gmail.com> wrote:
>
> > Dear Prof. Dan,
> >
> > Thank you very much for the suggestion. However, when I gave the command;
> > gmx select -f run05.xtc -s run05.tpr -b 39 -e 40 -on index.ndx in
> > VMD TkConsole, I didn't get any output.
> >
> > I didn't get the cursor in next line to type x > 45 and x < 90 and y > 90
> > and y. What could be the reason for this? Appreciate, if you can reply
> me.
> >
> > Thank you.
> >
> > On Fri, Sep 28, 2018 at 12:00 AM Dan Gil  wrote:
> >
> > > Hi,
> > >
> > > I believe you are trying to select atoms/particles that are in an
> > > infinitely tall box with the vertices (45, 90), (45, 125), (90, 90) and
> > > (90, 125)?
> > >
> > > Gmx select uses commands that are similar in syntax to a software
> called
> > > VMD. So I like to use VMD to figure out what I need to give to gmx
> select
> > > in order to get the selections I want.
> > >
> > > For example, I think for what you want, I would do:
> > >
> > > gmx select -f run05.xtc -s run05.tpr -b 39 -e 40 -on index.ndx
> > > [Press Enter]
> > > x > 45 and x < 90 and y > 90 and y < 125 [Press Enter]
> > >
> > > If you want to include it in a script without manual user input:
> > >
> > > echo x > 45 and x < 90 and y > 90 and y < 125 | gmx select -f run05.xtc
> > -s
> > > run05.tpr -b 39 -e 40 -on index.ndx
> > >
> > > VMD is great! It's also free software if you haven't tried using it
> yet.
> > > The only thing you gotta watch out for is that VMD uses Angstroms while
> > GMX
> > > uses nm.
> > >
> > > Dan
> > >
> > > On Thu, Sep 27, 2018 at 7:51 AM Shan Jayasinghe <
> > > shanjayasinghe2...@gmail.com> wrote:
> > >
> > > > Dear Gromacs users,
> > > >
> > > > I want to make an index files with molecules in a particular area. I
> > have
> > > > four x,y coordinates [(45, 90), (45, 125), (90, 90) and (90, 125)]
> > which
> > > > define an area of the system. How can I do it with gmx_select?
> > > >
> > > > Can anyone help me?
> > > >
> > > > Thank you.
> > > >
> > > > On Thu, Sep 27, 2018 at 4:14 PM Shan Jayasinghe <
> > > > shanjayasinghe2...@gmail.com> wrote:
> > > >
> > > > >
> > > > > Dear Gromacs users,
> > > > >
> > > > > I want to make an index files with particular x and y coordinates.
> > > There
> > > > > is no restriction for z coordinates. How can I do it with
> > gmx_select? I
> > > > > already tried with the following command. However, it seems I don't
> > get
> > > > the
> > > > > result I want.
> > > > >
> > > > > gmx select '[45, 90] and [45, 125] and [90, 90] and [90, 125]' -f
> > > > > run05.xtc -s run05.tpr -b 39 -e 40 -on index.ndx
> > > > >
> > > > > Can anyone help me?
> > > > >
> > > > > Thank you.
> > > > >
> > > >
> > > >
> > > > --
> > > > Best Regards
> > > > Shan Jayasinghe
> > > > --
> > > > Gromacs Users mailing list
> > > >
> > > > * Please search the archive at
> > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > > posting!
> > > >
> > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > >
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> > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> > > > send a mail to gmx-users-requ...@gromacs.org.
> > > >
> > > --
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> > > posting!
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> > > send a mail to gmx-users-requ...@gromacs.org.
> > >
> >
> >
> > --
> > Best Regards
> > Shan Jayasinghe
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
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> > send a mail to gmx-users-requ...@gromacs.org.
> >
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>


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Best Regards

Re: [gmx-users] gmx select with coordinates

[Dan Gil]

Hi Shan,

Sorry it's been a while - I don't check this email too often. Did you
figure the problem out?

I use the Graphical Representations menu of VMD, although I am sure there
is a way to do it in the console too.

On Thu, Sep 27, 2018 at 9:35 PM Shan Jayasinghe <
shanjayasinghe2...@gmail.com> wrote:

> Dear Prof. Dan,
>
> Thank you very much for the suggestion. However, when I gave the command;
> gmx select -f run05.xtc -s run05.tpr -b 39 -e 40 -on index.ndx in
> VMD TkConsole, I didn't get any output.
>
> I didn't get the cursor in next line to type x > 45 and x < 90 and y > 90
> and y. What could be the reason for this? Appreciate, if you can reply me.
>
> Thank you.
>
> On Fri, Sep 28, 2018 at 12:00 AM Dan Gil  wrote:
>
> > Hi,
> >
> > I believe you are trying to select atoms/particles that are in an
> > infinitely tall box with the vertices (45, 90), (45, 125), (90, 90) and
> > (90, 125)?
> >
> > Gmx select uses commands that are similar in syntax to a software called
> > VMD. So I like to use VMD to figure out what I need to give to gmx select
> > in order to get the selections I want.
> >
> > For example, I think for what you want, I would do:
> >
> > gmx select -f run05.xtc -s run05.tpr -b 39 -e 40 -on index.ndx
> > [Press Enter]
> > x > 45 and x < 90 and y > 90 and y < 125 [Press Enter]
> >
> > If you want to include it in a script without manual user input:
> >
> > echo x > 45 and x < 90 and y > 90 and y < 125 | gmx select -f run05.xtc
> -s
> > run05.tpr -b 39 -e 40 -on index.ndx
> >
> > VMD is great! It's also free software if you haven't tried using it yet.
> > The only thing you gotta watch out for is that VMD uses Angstroms while
> GMX
> > uses nm.
> >
> > Dan
> >
> > On Thu, Sep 27, 2018 at 7:51 AM Shan Jayasinghe <
> > shanjayasinghe2...@gmail.com> wrote:
> >
> > > Dear Gromacs users,
> > >
> > > I want to make an index files with molecules in a particular area. I
> have
> > > four x,y coordinates [(45, 90), (45, 125), (90, 90) and (90, 125)]
> which
> > > define an area of the system. How can I do it with gmx_select?
> > >
> > > Can anyone help me?
> > >
> > > Thank you.
> > >
> > > On Thu, Sep 27, 2018 at 4:14 PM Shan Jayasinghe <
> > > shanjayasinghe2...@gmail.com> wrote:
> > >
> > > >
> > > > Dear Gromacs users,
> > > >
> > > > I want to make an index files with particular x and y coordinates.
> > There
> > > > is no restriction for z coordinates. How can I do it with
> gmx_select? I
> > > > already tried with the following command. However, it seems I don't
> get
> > > the
> > > > result I want.
> > > >
> > > > gmx select '[45, 90] and [45, 125] and [90, 90] and [90, 125]' -f
> > > > run05.xtc -s run05.tpr -b 39 -e 40 -on index.ndx
> > > >
> > > > Can anyone help me?
> > > >
> > > > Thank you.
> > > >
> > >
> > >
> > > --
> > > Best Regards
> > > Shan Jayasinghe
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-requ...@gromacs.org.
> > >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
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> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
>
>
> --
> Best Regards
> Shan Jayasinghe
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
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>
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Re: [gmx-users] gmx select with coordinates

[Shan Jayasinghe]

Dear Prof. Dan,

Thank you very much for the suggestion. However, when I gave the command;
gmx select -f run05.xtc -s run05.tpr -b 39 -e 40 -on index.ndx in
VMD TkConsole, I didn't get any output.

I didn't get the cursor in next line to type x > 45 and x < 90 and y > 90
and y. What could be the reason for this? Appreciate, if you can reply me.

Thank you.

On Fri, Sep 28, 2018 at 12:00 AM Dan Gil  wrote:

> Hi,
>
> I believe you are trying to select atoms/particles that are in an
> infinitely tall box with the vertices (45, 90), (45, 125), (90, 90) and
> (90, 125)?
>
> Gmx select uses commands that are similar in syntax to a software called
> VMD. So I like to use VMD to figure out what I need to give to gmx select
> in order to get the selections I want.
>
> For example, I think for what you want, I would do:
>
> gmx select -f run05.xtc -s run05.tpr -b 39 -e 40 -on index.ndx
> [Press Enter]
> x > 45 and x < 90 and y > 90 and y < 125 [Press Enter]
>
> If you want to include it in a script without manual user input:
>
> echo x > 45 and x < 90 and y > 90 and y < 125 | gmx select -f run05.xtc -s
> run05.tpr -b 39 -e 40 -on index.ndx
>
> VMD is great! It's also free software if you haven't tried using it yet.
> The only thing you gotta watch out for is that VMD uses Angstroms while GMX
> uses nm.
>
> Dan
>
> On Thu, Sep 27, 2018 at 7:51 AM Shan Jayasinghe <
> shanjayasinghe2...@gmail.com> wrote:
>
> > Dear Gromacs users,
> >
> > I want to make an index files with molecules in a particular area. I have
> > four x,y coordinates [(45, 90), (45, 125), (90, 90) and (90, 125)] which
> > define an area of the system. How can I do it with gmx_select?
> >
> > Can anyone help me?
> >
> > Thank you.
> >
> > On Thu, Sep 27, 2018 at 4:14 PM Shan Jayasinghe <
> > shanjayasinghe2...@gmail.com> wrote:
> >
> > >
> > > Dear Gromacs users,
> > >
> > > I want to make an index files with particular x and y coordinates.
> There
> > > is no restriction for z coordinates. How can I do it with gmx_select? I
> > > already tried with the following command. However, it seems I don't get
> > the
> > > result I want.
> > >
> > > gmx select '[45, 90] and [45, 125] and [90, 90] and [90, 125]' -f
> > > run05.xtc -s run05.tpr -b 39 -e 40 -on index.ndx
> > >
> > > Can anyone help me?
> > >
> > > Thank you.
> > >
> >
> >
> > --
> > Best Regards
> > Shan Jayasinghe
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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>


-- 
Best Regards
Shan Jayasinghe
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Re: [gmx-users] gmx select with coordinates

[Dan Gil]

Hi,

I believe you are trying to select atoms/particles that are in an
infinitely tall box with the vertices (45, 90), (45, 125), (90, 90) and
(90, 125)?

Gmx select uses commands that are similar in syntax to a software called
VMD. So I like to use VMD to figure out what I need to give to gmx select
in order to get the selections I want.

For example, I think for what you want, I would do:

gmx select -f run05.xtc -s run05.tpr -b 39 -e 40 -on index.ndx
[Press Enter]
x > 45 and x < 90 and y > 90 and y < 125 [Press Enter]

If you want to include it in a script without manual user input:

echo x > 45 and x < 90 and y > 90 and y < 125 | gmx select -f run05.xtc -s
run05.tpr -b 39 -e 40 -on index.ndx

VMD is great! It's also free software if you haven't tried using it yet.
The only thing you gotta watch out for is that VMD uses Angstroms while GMX
uses nm.

Dan

On Thu, Sep 27, 2018 at 7:51 AM Shan Jayasinghe <
shanjayasinghe2...@gmail.com> wrote:

> Dear Gromacs users,
>
> I want to make an index files with molecules in a particular area. I have
> four x,y coordinates [(45, 90), (45, 125), (90, 90) and (90, 125)] which
> define an area of the system. How can I do it with gmx_select?
>
> Can anyone help me?
>
> Thank you.
>
> On Thu, Sep 27, 2018 at 4:14 PM Shan Jayasinghe <
> shanjayasinghe2...@gmail.com> wrote:
>
> >
> > Dear Gromacs users,
> >
> > I want to make an index files with particular x and y coordinates. There
> > is no restriction for z coordinates. How can I do it with gmx_select? I
> > already tried with the following command. However, it seems I don't get
> the
> > result I want.
> >
> > gmx select '[45, 90] and [45, 125] and [90, 90] and [90, 125]' -f
> > run05.xtc -s run05.tpr -b 39 -e 40 -on index.ndx
> >
> > Can anyone help me?
> >
> > Thank you.
> >
>
>
> --
> Best Regards
> Shan Jayasinghe
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
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Re: [gmx-users] gmx select with coordinates

[Shan Jayasinghe]

Dear Gromacs users,

I want to make an index files with molecules in a particular area. I have
four x,y coordinates [(45, 90), (45, 125), (90, 90) and (90, 125)] which
define an area of the system. How can I do it with gmx_select?

Can anyone help me?

Thank you.

On Thu, Sep 27, 2018 at 4:14 PM Shan Jayasinghe <
shanjayasinghe2...@gmail.com> wrote:

>
> Dear Gromacs users,
>
> I want to make an index files with particular x and y coordinates. There
> is no restriction for z coordinates. How can I do it with gmx_select? I
> already tried with the following command. However, it seems I don't get the
> result I want.
>
> gmx select '[45, 90] and [45, 125] and [90, 90] and [90, 125]' -f
> run05.xtc -s run05.tpr -b 39 -e 40 -on index.ndx
>
> Can anyone help me?
>
> Thank you.
>


-- 
Best Regards
Shan Jayasinghe
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[gmx-users] gmx select with coordinates

[Shan Jayasinghe]

Dear Gromacs users,

I want to make an index files with particular x and y coordinates. There is
no restriction for z coordinates. How can I do it with gmx_select? I
already tried with the following command. However, it seems I don't get the
result I want.

gmx select '[45, 90] and [45, 125] and [90, 90] and [90, 125]' -f run05.xtc
-s run05.tpr -b 39 -e 40 -on index.ndx

Can anyone help me?

Thank you.
-- 
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Re: [gmx-users] gmx select and gmx trjconv or gmx density

[Dan Gil]

Thank you Dr. Abraham!

I think I will write a script to do the analysis then.

Best Regards,

Dan

On Mon, Apr 9, 2018 at 12:57 PM, Mark Abraham 
wrote:

> Hi,
>
> Unfortunately not all tools support dynamic selection groups yet, so the
> only useful way to use that index file is by matching it with the correct
> single frame from the trajectory, which you might get from e.g. gmx trjconv
> split
>
> Mark
>
> On Fri, Apr 6, 2018, 21:37 Dan Gil  wrote:
>
> > Hi,
> >
> > I am trying to select particles that are z < 20 and z > 10 as a function
> of
> > time.
> >
> > I think I used gmx select correctly and generated an index file with
> group
> > names like "(z_<_.8_f2882_t23056.000)"
> >
> > Now I am unsure how I use this index file for gmx trjconv or gmx density.
> > Does anybody have some advice?
> >
> > Thanks in advance.
> >
> > Best Regards,
> >
> > Dan Gil
> > PhD Student
> > Case Western Reserve University
> > Department of Chemical and Biomolecular Engineering
> > --
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Re: [gmx-users] gmx select and gmx trjconv or gmx density

[Mark Abraham]

Hi,

Unfortunately not all tools support dynamic selection groups yet, so the
only useful way to use that index file is by matching it with the correct
single frame from the trajectory, which you might get from e.g. gmx trjconv
split

Mark

On Fri, Apr 6, 2018, 21:37 Dan Gil  wrote:

> Hi,
>
> I am trying to select particles that are z < 20 and z > 10 as a function of
> time.
>
> I think I used gmx select correctly and generated an index file with group
> names like "(z_<_.8_f2882_t23056.000)"
>
> Now I am unsure how I use this index file for gmx trjconv or gmx density.
> Does anybody have some advice?
>
> Thanks in advance.
>
> Best Regards,
>
> Dan Gil
> PhD Student
> Case Western Reserve University
> Department of Chemical and Biomolecular Engineering
> --
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[gmx-users] gmx select and gmx trjconv or gmx density

[Dan Gil]

Hi,

I am trying to select particles that are z < 20 and z > 10 as a function of
time.

I think I used gmx select correctly and generated an index file with group
names like "(z_<_.8_f2882_t23056.000)"

Now I am unsure how I use this index file for gmx trjconv or gmx density.
Does anybody have some advice?

Thanks in advance.

Best Regards,

Dan Gil
PhD Student
Case Western Reserve University
Department of Chemical and Biomolecular Engineering
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[gmx-users] gmx select querry

[shivangi nangia]

Hello All,


I have a question regarding the usage of gmx select.


I want to select water molecules in a particular subset in z-direction
(example z > 5 and z < 10) for each frame of my trajectory and then carry
out analysis using g_mindist on each frame of the trajectory (with
selections)

For example: system consists of peptide 1 and peptide2, membrane, water and
ions.

using g_mindist, I want to calculate the number of contacts peptide1 is
making with water vs. peptide2 in z >5 and z < 10 over the whole trajectory.

When I try to make selection using:
The option pdbatoms selected only lists the selected atoms.
The option pdbatoms all lists everything.

The -on options gives me the index file of only selected atoms:

gmx_mpi select -f 432000g1.gro -s ../../3run_npt_noposre.tpr -select
'(resname TIP3 and name OH2) and z  > -10 and z < 20'  -oi -pdbatoms
selected -on insel.ndx
I am a little confused how to incoporate the slections in odere to carry
out the analysis I am interested in.

Kindly suggest.

Thanks for your time in advance.

Regards,
sn
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Re: [gmx-users] gmx select

[Justin Lemkul]

On 7/13/17 10:01 AM, Pandya, Akash wrote:

So I tried with both opening and closing. It seems to select all the molecules 
in my box which is not what I want. I only want certain glycine molecules that 
are closest to the protein. May you please suggest another way is which I could 
achieve this. The command I used is below:

gmx select -f output.xtc -s output.gro -select '"Close to protein" resname Glycine and 
within 0.5 of group "Protein"' -pdbatoms selected -ofpdb



"resname Glycine" surely will return nothing.  You need to use valid residue 
names as found in the .gro file.  The format of .gro permits residue names up to 
5 characters, so clearly "Glycine" is never going to match anything.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] gmx select

[Pandya, Akash]

So I tried with both opening and closing. It seems to select all the molecules 
in my box which is not what I want. I only want certain glycine molecules that 
are closest to the protein. May you please suggest another way is which I could 
achieve this. The command I used is below:

gmx select -f output.xtc -s output.gro -select '"Close to protein" resname 
Glycine and within 0.5 of group "Protein"' -pdbatoms selected -ofpdb 

Akash


-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin 
Lemkul
Sent: 13 July 2017 14:01
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] gmx select



On 7/13/17 3:38 AM, Pandya, Akash wrote:
> gmx select -f output.gro -select "Close to protein" resname Glyci and within 
> 0.5 of group "Protein"'
> 

I suspect Mark is right, this is an invalid command, because you have a closing 
' without an opening ' in your -select argument.  This should fail with a 
generic error message that the selection can't be parsed.  I am also curious 
about "resname Glyci" because if that's the case, then you must have hacked 
some force field files, because everyone calls glycine "GLY" per standard 
nomenclature.

-Justin

> -Original Message-
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
> [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf 
> Of Mark Abraham
> Sent: 13 July 2017 00:04
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] gmx select
> 
> Hi,
> 
> Can you please copy, paste and post your actual commands. I don't think your 
> use of quote marks would have led to a valid shell command. The whole 
> selection text will need to be inside some quotes.
> 
> Mark
> 
> On Wed, 12 Jul 2017 23:47 Pandya, Akash <akash.pandya...@ucl.ac.uk> wrote:
> 
>> I have used the same name in my coordinate file. For Glycine it is 
>> spelt as Glyci, so the word has been cut off. I know this is correct 
>> because I use the same name in VMD.
>>
>> -Original Message-
>> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
>> gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark 
>> Abraham
>> Sent: 12 July 2017 22:42
>> To: gmx-us...@gromacs.org
>> Subject: Re: [gmx-users] gmx select
>>
>> Hi,
>>
>> What are the residue names in your coordinate file? Glyci probably 
>> doesn't fit
>>
>> Mark
>>
>> On Wed, Jul 12, 2017 at 10:36 PM Pandya, Akash 
>> <akash.pandya...@ucl.ac.uk>
>> wrote:
>>
>>> Hi all,
>>>
>>>
>>> I am trying to select all the glycine molecules with 0.5nm of my protein.
>>> I tried both of these commands I got from the gromacs website:
>>>
>>> gmx select -f output.gro -select "Close to protein" resname Glyci 
>>> and within 0.5 of group "Protein"' -ofpdb
>>>
>>> gmx select -f output.xtc -s output.tpr (my converted input file) 
>>> -select "Close to protein" resname Glyci and within 0.5 of group 
>>> "Protein"' -ofpdb
>>>
>>>
>>> Nothing comes up when I enter them. Please could someone help me 
>>> with
>> this?
>>>
>>>
>>> Akash
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before 
>>> posting!
>>>
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>>> or send a mail to gmx-users-requ...@gromacs.org.
>>>
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>> send a mail to gmx-users

Re: [gmx-users] gmx select

[Justin Lemkul]

On 7/13/17 3:38 AM, Pandya, Akash wrote:

gmx select -f output.gro -select "Close to protein" resname Glyci and within 0.5 of group 
"Protein"'



I suspect Mark is right, this is an invalid command, because you have a closing 
' without an opening ' in your -select argument.  This should fail with a 
generic error message that the selection can't be parsed.  I am also curious 
about "resname Glyci" because if that's the case, then you must have hacked some 
force field files, because everyone calls glycine "GLY" per standard nomenclature.


-Justin


-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark 
Abraham
Sent: 13 July 2017 00:04
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] gmx select

Hi,

Can you please copy, paste and post your actual commands. I don't think your 
use of quote marks would have led to a valid shell command. The whole selection 
text will need to be inside some quotes.

Mark

On Wed, 12 Jul 2017 23:47 Pandya, Akash <akash.pandya...@ucl.ac.uk> wrote:


I have used the same name in my coordinate file. For Glycine it is
spelt as Glyci, so the word has been cut off. I know this is correct
because I use the same name in VMD.

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark
Abraham
Sent: 12 July 2017 22:42
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] gmx select

Hi,

What are the residue names in your coordinate file? Glyci probably
doesn't fit

Mark

On Wed, Jul 12, 2017 at 10:36 PM Pandya, Akash
<akash.pandya...@ucl.ac.uk>
wrote:


Hi all,


I am trying to select all the glycine molecules with 0.5nm of my protein.
I tried both of these commands I got from the gromacs website:

gmx select -f output.gro -select "Close to protein" resname Glyci
and within 0.5 of group "Protein"' -ofpdb

gmx select -f output.xtc -s output.tpr (my converted input file)
-select "Close to protein" resname Glyci and within 0.5 of group
"Protein"' -ofpdb


Nothing comes up when I enter them. Please could someone help me
with

this?



Akash
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--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] gmx select

[Pandya, Akash]

gmx select -f output.gro -select "Close to protein" resname Glyci and within 
0.5 of group "Protein"'

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark 
Abraham
Sent: 13 July 2017 00:04
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] gmx select

Hi,

Can you please copy, paste and post your actual commands. I don't think your 
use of quote marks would have led to a valid shell command. The whole selection 
text will need to be inside some quotes.

Mark

On Wed, 12 Jul 2017 23:47 Pandya, Akash <akash.pandya...@ucl.ac.uk> wrote:

> I have used the same name in my coordinate file. For Glycine it is 
> spelt as Glyci, so the word has been cut off. I know this is correct 
> because I use the same name in VMD.
>
> -Original Message-
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark 
> Abraham
> Sent: 12 July 2017 22:42
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] gmx select
>
> Hi,
>
> What are the residue names in your coordinate file? Glyci probably 
> doesn't fit
>
> Mark
>
> On Wed, Jul 12, 2017 at 10:36 PM Pandya, Akash 
> <akash.pandya...@ucl.ac.uk>
> wrote:
>
> > Hi all,
> >
> >
> > I am trying to select all the glycine molecules with 0.5nm of my protein.
> > I tried both of these commands I got from the gromacs website:
> >
> > gmx select -f output.gro -select "Close to protein" resname Glyci 
> > and within 0.5 of group "Protein"' -ofpdb
> >
> > gmx select -f output.xtc -s output.tpr (my converted input file) 
> > -select "Close to protein" resname Glyci and within 0.5 of group 
> > "Protein"' -ofpdb
> >
> >
> > Nothing comes up when I enter them. Please could someone help me 
> > with
> this?
> >
> >
> > Akash
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before 
> > posting!
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> > or send a mail to gmx-users-requ...@gromacs.org.
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Re: [gmx-users] gmx select

[Mark Abraham]

Hi,

Can you please copy, paste and post your actual commands. I don't think
your use of quote marks would have led to a valid shell command. The whole
selection text will need to be inside some quotes.

Mark

On Wed, 12 Jul 2017 23:47 Pandya, Akash <akash.pandya...@ucl.ac.uk> wrote:

> I have used the same name in my coordinate file. For Glycine it is spelt
> as Glyci, so the word has been cut off. I know this is correct because I
> use the same name in VMD.
>
> -Original Message-
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark
> Abraham
> Sent: 12 July 2017 22:42
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] gmx select
>
> Hi,
>
> What are the residue names in your coordinate file? Glyci probably doesn't
> fit
>
> Mark
>
> On Wed, Jul 12, 2017 at 10:36 PM Pandya, Akash <akash.pandya...@ucl.ac.uk>
> wrote:
>
> > Hi all,
> >
> >
> > I am trying to select all the glycine molecules with 0.5nm of my protein.
> > I tried both of these commands I got from the gromacs website:
> >
> > gmx select -f output.gro -select "Close to protein" resname Glyci and
> > within 0.5 of group "Protein"' -ofpdb
> >
> > gmx select -f output.xtc -s output.tpr (my converted input file)
> > -select "Close to protein" resname Glyci and within 0.5 of group
> > "Protein"' -ofpdb
> >
> >
> > Nothing comes up when I enter them. Please could someone help me with
> this?
> >
> >
> > Akash
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
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> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
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Re: [gmx-users] gmx select

[Pandya, Akash]

I have used the same name in my coordinate file. For Glycine it is spelt as 
Glyci, so the word has been cut off. I know this is correct because I use the 
same name in VMD.   

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark 
Abraham
Sent: 12 July 2017 22:42
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] gmx select

Hi,

What are the residue names in your coordinate file? Glyci probably doesn't fit

Mark

On Wed, Jul 12, 2017 at 10:36 PM Pandya, Akash <akash.pandya...@ucl.ac.uk>
wrote:

> Hi all,
>
>
> I am trying to select all the glycine molecules with 0.5nm of my protein.
> I tried both of these commands I got from the gromacs website:
>
> gmx select -f output.gro -select "Close to protein" resname Glyci and 
> within 0.5 of group "Protein"' -ofpdb
>
> gmx select -f output.xtc -s output.tpr (my converted input file) 
> -select "Close to protein" resname Glyci and within 0.5 of group 
> "Protein"' -ofpdb
>
>
> Nothing comes up when I enter them. Please could someone help me with this?
>
>
> Akash
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Re: [gmx-users] gmx select

[Mark Abraham]

Hi,

What are the residue names in your coordinate file? Glyci probably doesn't
fit

Mark

On Wed, Jul 12, 2017 at 10:36 PM Pandya, Akash 
wrote:

> Hi all,
>
>
> I am trying to select all the glycine molecules with 0.5nm of my protein.
> I tried both of these commands I got from the gromacs website:
>
> gmx select -f output.gro -select "Close to protein" resname Glyci and
> within 0.5 of group "Protein"' -ofpdb
>
> gmx select -f output.xtc -s output.tpr (my converted input file) -select
> "Close to protein" resname Glyci and within 0.5 of group "Protein"' -ofpdb
>
>
> Nothing comes up when I enter them. Please could someone help me with this?
>
>
> Akash
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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[gmx-users] gmx select

[Pandya, Akash]

Hi all,


I am trying to select all the glycine molecules with 0.5nm of my protein. I 
tried both of these commands I got from the gromacs website:

gmx select -f output.gro -select "Close to protein" resname Glyci and within 
0.5 of group "Protein"' -ofpdb

gmx select -f output.xtc -s output.tpr (my converted input file) -select "Close 
to protein" resname Glyci and within 0.5 of group "Protein"' -ofpdb


Nothing comes up when I enter them. Please could someone help me with this?


Akash
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[gmx-users] gmx select

[Nicolas Cheron]

Dear all,

I am a little bit lost with the use of select. I am looking at a protein in
a water:glycerol mixture. I would like to count how many glycerol molecules
there are within 3Angstrom of the protein. I first used the following
command to count the central atom (named C2):

gmx select -s File.gro -f File.xtc -n Index.ndx -os Gly-0.3.xvg -xvg none
-select "name C2 and within 0.3 of group Protein"

This gives me on average over the trajectory 3.3. Then I wanted to count
for the center of mass of glycerols, which shouldn't be too far from the
central atom:

gmx select -s File.gro -f File.xtc -n Index.ndx -os Gly-0.3.xvg -xvg none
-select "res_com of resname GOL and within 0.3 of group Protein"

There I found 58.4. I got the same result with whole_res_com than with
res_com, and with Gromacs 5.1.1, 5.1.2 and 2016.

I am surprised by the difference. I suspect that the second command counts
all the atoms. Can someone please tell me if the last command is correct,
and if not tell me what would be the correct use of select to count the
number of center of mass of the glycerol molecules that have their center
of mass within 0.3nm of the protein.

Thank you

Nicolas

PS: I posted this question on the list a week ago but not sure it went
through, sorry for the double posting
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