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

Justin A. Lemkul Wed, 12 May 2010 12:31:58 -0700


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, thenchoose EMI for both the calculation and output group for g_spatial, you shouldget an isosurface of just the position of EMI, it shouldn't overlap with theglucose molecule if the fitting was done properly.

Have you loaded the data correctly? If you render the glucose and EMIseparately, 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 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