[gmx-users] peptide ligand

[farial tavakoli]

 blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px #715FFA solid !important; padding-left:1ex !important; background-color:white !important; }  Then I ignore that  i cant visualize the protein motion in vmd and go on the left steps of the results quality assuranc?


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On Friday, November 10, 2017, 7:35 PM, Justin Lemkul <jalemkul at vt.edu> wrote:



On 11/10/17 11:02 AM, farial tavakoli wrote:
>  blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px #715FFA solid !important; padding-left:1ex !important; background-color:white !important; }  so how come i bring the .gro and newtrj.xtc files in the vmd , my protein doesnt move at all? I think , it is because of the .gro file has protein, ligand and sol cordinates , but the newtrj.xtc has just my protein and ligand. Am i right?
>  

Your trajectory and coordinates have to match if you want to visualize. 
If there's a mismatch, VMD prints a clear error that should tell you of 
that fact.

-Justin

>
>      On Friday, November 10, 2017, 7:20:48 PM GMT+3:30, Justin Lemkul <jalemkul at vt.edu> wrote:
>  
>  
>
> On 11/10/17 10:35 AM, farial tavakoli wrote:
>> Dear Justin
>>
>> Thank you for replying
>>
>> This is my input xtc file :
>>
>> gmx check -f md_0_1.xtc
>>
>> Checking file md_0_1.xtc
>> Reading frame       0 time    0.000
>> # Atoms  49582
>> Precision 0.001 (nm)
>> Last frame       1000 time 10000.000
>>
>>
>> Item        #frames Timestep (ps)
>> Step          1001    10
>> Time          1001    10
>> Lambda           0
>> Coords        1001    10
>> Velocities       0
>> Forces           0
>> Box           1001    10
>>
>> and this is my output xtc file:
>>
>> gmx check -f newtrj.xtc
>>
>> Checking file newtrj.xtc
>> Reading frame       0 time    0.000
>> # Atoms  3378
>> Precision 0.001 (nm)
>> Last frame       1000 time 10000.000
>>
>>
>> Item        #frames Timestep (ps)
>> Step          1001    10
>> Time          1001    10
>> Lambda           0
>> Coords        1001    10
>> Velocities       0
>> Forces           0
>> Box           1001    10
>>
> These outputs do not support your assertion that newtrj.xtc only
> contains one frame. Clearly both the old and new trajectories have the
> full 1001 frames.
>
> -Justin
>

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

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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