lina wrote:
make_ndx -f your.gro/pdb -n your.ndx -o your.ndx
LiGA & LİGB:
This is not correct. You need to use | rather than &. Using logical and (&)
means the index group will contain atoms that are common to both LIGA and LIGB.
If they are distinct entities, the group will be empty. Logical or (|) says
merge the two different groups to create one unified group.
-Justin
q
in grompp add -n your.ndx
2011/5/12 ahmet yıldırım <ahmedo...@gmail.com>:
Dear users,
I have two ligands. I created a special index group that merges the protein,
LiGA and LİGB.
I have the pr.mdp file as the following:
...
energygrps = Protein LİGA_LİGB
tc-grps = Protein_LİGA_LİGB Water_and_ions
...
grompp -f pr.mdp -p topol.top -c em.gro -n index.ndx -o pr.tpr
Fatal error:
Group LİGA_LİGB not found in indexfile.
I get the fatal error since I dont have a special index group that merges
LiGA and LİGB. should I create two different index file?
Thanks in advance
--
Ahmet YILDIRIM
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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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