[gmx-users] trjconv : error
Nilesh Dhumal
ndhumal at andrew.cmu.edu
Wed May 12 19:34:14 CEST 2010
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
After this I followed the steps given in g_spatial -h.
I selected residue Group 14 and EMI is Group 39 for trjconv.
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).
As I want to plot how glucose (GLU:Group 14 )is surrounded by cation
(EMI:Group 39).
Should I select Group 14 in tpbconv ?
Sorry for so much details and your help is really appreciated.
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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