Re: Re : [gmx-users] trjconv : error

Justin A. Lemkul Wed, 12 May 2010 14:52:46 -0700


Nilesh Dhumal wrote:

Hello Justin,

Using gmxcheck I checked the number of atoms in trajectory. I got the
correct no.

I am still stuck with trjconv.

1. trjconv -s test.tpr  -f 3.xtc -o b.xtc -center  -ur compact -pbc none
-n glu-emi-cl-128-no.ndx

for above command I selected  Group 14 from .ndx file which is glucose
molecule I want to centered.

Pay attention to the prompts. There is a second prompt to choose the group youwant output. If you choose glucose here, you will only get glucose coordinateswritten to the trajectory - trjconv will do what you tell it! For now, alwayschoose System as the group for output.

2.  trjconv -s 3.tpr  -f b.xtc -o c.xtc -fit rot+trans  -dt 500 -n test.ndx

for this command 1st I selected Group 14 (Glucose)and 2nd is Group 39
(EMI)cation. For this command I got this error.

Fatal error:Index[0] 25 is larger than the number of atoms in the
trajectory file (24)

Yes, because in step 1 above, you saved only glucose coordinates. Therefore, inb.xtc, nothing else exists.


-Justin

Nilesh





On Wed, May 12, 2010 3:30 pm, Justin A. Lemkul wrote:

Nilesh Dhumal wrote:

Ok. Justin.
I am centering  group 14 (glucose) and EMI is your output group.
If I do g_spatial it works well.
g_spatial -f 3.xtc -n glu-emi-cl-128-no.ndx -s 3.tpr

After loading grid.cube in vmd, I could see whole system. I was
expecting that I can see  glucose and can plot iso-surface to explain
the position of cation.

I don't understand why this is happening.  If you do the fitting
procedure, then choose EMI for both the calculation and output group for
g_spatial, you should get an isosurface of just the position of EMI, it
shouldn't overlap with the glucose molecule if the fitting was done
properly.

Have you loaded the data correctly?  If you render the glucose and EMI
separately, then load the .cube file into it and display EMI as
"Isosurface,"
you should get the visualization you want.

-Justin

Nilesh

Do you
give these same groups for both #1 and #2 below?  What if you output
the entire system?  The only time you should need to use your special
index group is for g_spatial itself, as the group to use in the
calculation.



On Wed, May 12, 2010 1:48 pm, Justin A. Lemkul wrote:

Nilesh Dhumal wrote:

Hello Justin



tpbconv -f 3.trr -s 3.tpr -e 3.edr -n glu-emi-cl-128-no.ndx -o
test.tpr


Group     0 (      System) has  2584 elements
Group     1 (     Protein) has  2456 elements
Group     2 (   Protein-H) has  1036 elements
Group     3 (     C-alpha) has     0 elements
Group     4 (    Backbone) has   128 elements
Group     5 (   MainChain) has   129 elements
Group     6 (MainChain+Cb) has   129 elements
Group     7 ( MainChain+H) has   129 elements
Group     8 (   SideChain) has  2327 elements
Group     9 ( SideChain-H) has   907 elements
Group    10 ( Prot-Masses) has  2456 elements
Group    11 ( Non-Protein) has   128 elements
Group    12 (          CL) has   128 elements
Group    13 (       Other) has   128 elements
Group    14 (         GUL) has    24 elements
Group    15 (           O) has     1 elements
--




---
Group    39 (         EMI) has  2432 elements
Group    40 (           C) has   128 elements
---
----
Group    57 (         H18) has   128 elements
Group    58 (         H19) has   128 elements
Group    59 (          CL) has   128 elements
Group    60 (          CL) has   128 elements




I selected Group 0

As I said before, selecting "System" when running tpbconv to get some
 subset of atoms is pointless.  For now, please abandon the use of
tpbconv altogether.  I will repeat: I do not think this is the best
approach for you to use, and is probably just confusing right now.

The output indicates that you have 2584 atoms accounted for in your
original .tpr file.  How many atoms are in your trajectory (using
gmxcheck)?

After this I followed the steps given in g_spatial -h.



I selected residue Group 14 and EMI is Group 39 for trjconv.

So, group 14 (glucose) is for centering, and EMI is your output
group? Do you
give these same groups for both #1 and #2 below?  What if you output
the entire system?  The only time you should need to use your special
index group is for g_spatial itself, as the group to use in the
calculation.

1. trjconv -s test.tpr  -f 3.xtc -o b.xtc -center  -ur compact -pbc
 none -n glu-emi-cl-128-no.ndx


2. trjconv -s test.tpr  -f b.xtc -o c.xtc -fit rot+trans -n
glu-emi-cl-128-no.ndx


For 2nd step I got the error



Fatal error: Index[2385] 2410 is larger than the number of atoms in
 the trajectory file (2409).

This is a consequence of previously outputting some subset of the
atoms above.

As I want to plot how glucose (GLU:Group 14 )is surrounded by
cation (EMI:Group 39).



Should I select Group 14 in tpbconv ?

No, please discontinue any thought of using tpbconv altogether.

Sorry for so much details and your help is really appreciated.

More detail is better.  The more complete the thread is, the more it
helps others and the faster you get a resolution.

-Justin

Thanks
Nilesh





On Wed, May 12, 2010 10:58 am, [email protected] wrote:

Hi Nilesh,
If you need the whole system you maybe don't need to include the
-n
flag in the tpbconv command it will still create your new tpr file
for continuing your work without errors, I had earlier some
similar problem. But as Justin mentioned it is due to some
specification in the mpd as for part of your system was selected
only.. Gigi









-----E-mail d'origine-----
De : Nilesh Dhumal <[email protected]>
A : [email protected]; Discussion list for GROMACS users
<[email protected]>
EnvoyÃ© le : Mercredi, 12 Mai 2010 17:47
Sujet : Re: [gmx-users] trjconv : error





Hello Justin,
As you suggest I used tbpconv




tpbconv -f 3.trr -s 3.tpr -e 3.edr -n glu-emi-cl-128-no.ndx -o
test.tpr and I selected group 0 for system group (In system group
all atoms are present.)

Still I am getting the same error.





I have one more question,
I am working on solvation glucose in ionic liquids. As I told you
I
want to show glucose surrounded by cation using iso-surface. After
 loading grid.cub file in vmd, all atoms are present. How can I
do sothat I can get only glucose and plot the iso-surface to show
cation position. Can you help me to solve this problem.

Thanks
Nilesh




On Tue, May 11, 2010 5:22 pm, Justin A. Lemkul wrote:

Nilesh Dhumal wrote:

Hello,
I am trying to calculate spatial distribution function (SDF)
for my system.

1. trjconv -s 3.tpr -f 3.trr -o b.xtc -center -ur compact
-pbc
none -n test.ndx 2. rajconv -s 3.tpr -f b.xtc -o c.xtc - fit
rot+trans -n test.ndx

I am getting the following error for step 2.





Fatal error: Index[2385] 2410 is larger than the number of
atoms in the trajectory file (2409).

How can I solve this problem?
Duirng my simulation I didn't specify xtc_grps  this option in
md file.

Then it looks like you must have saved only a subset of your
system during step 1 or some other post-processing step.  Either
save the whole system, or use tpbconv to generate a .tpr file
that contains only the relevant subset of atoms.

-Justin

Thanks





Nilesh

--
========================================





Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin





========================================
--
gmx-users mailing list    [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search
before posting! Please don't post (un)subscribe requests to the
list. Use the www interface or send it to
[email protected]. Can't post? Read
http://www.gromacs.org/mailing_lists/users.php

--
gmx-users mailing list    [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before
posting! Please don't post (un)subscribe requests to the list. Use
the www interface or send it to [email protected].
Can't
post? Read http://www.gromacs.org/mailing_lists/users.php




--
gmx-users mailing list    [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before
posting! Please don't post (un)subscribe requests to the list. Use
the www interface or send it to [email protected].
Can't
post? Read http://www.gromacs.org/mailing_lists/users.php

--
========================================



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin



========================================
--
gmx-users mailing list    [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before
posting! Please don't post (un)subscribe requests to the list. Use the
 www interface or send it to [email protected]. Can't
post? Read http://www.gromacs.org/mailing_lists/users.php

--
========================================


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


========================================
--
gmx-users mailing list    [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
 Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected]. Can't post? Read
http://www.gromacs.org/mailing_lists/users.php


--
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================
--
gmx-users mailing list    [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!

Please don't post (un)subscribe requests to the list. Use thewww interface or send it to [email protected].

Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: Re : [gmx-users] trjconv : error

Reply via email to