[gmx-users] trjconv : error
Justin A. Lemkul
jalemkul at vt.edu
Wed May 12 21:30:20 CEST 2010
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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