[gmx-users] trjconv : error

Nilesh Dhumal ndhumal at andrew.cmu.edu
Wed May 12 21:11:21 CEST 2010 

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.

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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>>
>>
>
> --
> ========================================
>
>
> 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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