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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