[gmx-users] trjconv : error

Justin A. Lemkul jalemkul at vt.edu
Wed May 12 19:48:02 CEST 2010 


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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> 
> 

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

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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