[gmx-users] trjconv : error

Justin A. Lemkul jalemkul at vt.edu
Wed May 12 23:50:47 CEST 2010 


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 you 
want output.  If you choose glucose here, you will only get glucose coordinates 
written to the trajectory - trjconv will do what you tell it!  For now, always 
choose 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, in 
b.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, gigitang5 at aol.fr 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 <ndhumal at andrew.cmu.edu>
>>>>>> A : jalemkul at vt.edu; Discussion list for GROMACS users
>>>>>> <gmx-users at gromacs.org>
>>>>>> 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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>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>> --
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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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>>>>
>>>>
>>>
>>>
>> --
>> ========================================
>>
>>
>> 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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