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]>
Envoyé 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
========================================
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========================================
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
========================================
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