[gmx-users] trjconv : error
Nilesh Dhumal
ndhumal at andrew.cmu.edu
Wed May 12 23:39:27 CEST 2010
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.
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)
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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