[gmx-users] trjconv:solute at the center

[Justin A. Lemkul]

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

-- 
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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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