[gmx-users] trjconv:solute at the center

[Nilesh Dhumal]

In 2nd step I choose system instaed of solvent.

 I could not make the solute at the center.

Thanks
NIlesh

On Mon, October 17, 2011 11:05 am, Justin A. Lemkul wrote:
>

>
> Nilesh Dhumal wrote:
>
>> Justin,
>>
>>
>> I have 26 solute atoms and 3302 solvent atoms in my sytems (total 3328
>> atoms).
>>
>>
>> 1. trjconv -f 3.trr -s 3.tpr -pbc mol -b 400 -e 600 -dt 1 -n 500-1.ndx
>> -o
>> 4-600.xtc
>> here I choose group 0:system (3328 atoms)
>>
>> 2. trjconv -f 4-600.xtc -s 3.tpr  -n 500-1.ndx -center  -o 4-600-1.xtc
>>
>>
>> For Centering I choose group: solute (26 atoms)
>> For output I choose group : Solvent (3302 atoms)
>>
>>
>>
>> 3. trjconv -f 4-600-1.xtc -s 3.tpr  -dump 500  -o 500-11.pdb
>>
>>
>> Here I choose the group: 0 (system).
>>
>>
>> I am geting for error for last command.
>>
>>
>> Fatal error:
>> Index[3302] 3303 is larger than the number of atoms in the trajectory
>> file (3302).
>>
>>
>> It look that there are no solute atoms in trajectory file.
>>
>>
>
> In step 2, you chose to save only the solvent.
>
>
> -Justin
>
>
> --
> ========================================
>
>
> 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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