fahimeh bafti wrote:
Hello,
I want to use a file.pdb which has 8 chain of polypeptide, each chain
contains 6 residues. I need to expand it to 12 chains of 6 rsidues so I
need to add 4 chains or in the other word 24 residues. I think I have to
use genbox, so I make another copy of file.pdb and rename it to
insert.pdb and i used this command, but it doesn't work.
genbox -cp file.pdb -ci insert.pdb -nmole 24 -o out.gro
can anybody help me?
The implication with genbox -ci -nmol is that the coordinate file passed to -ci
contains one molecule, and an additional -nmol molecules are inserted. So if
you already have 8, you need a coordinate file with one polypeptide and then:
genbox -ci insert.pdb -nmol 4
Note in the documentation that -nmol refers to the number of molecules, not a
number of residues, which I think is the root of your problem.
-Justin
Fahimeh
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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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