Hi,
Thank you for your advices.The A-chain is topologically similar to the
activation peptide of chymotrypsin(ogen) and connected in a similar manner
through the Cys1Cys122 disulfide bridge to the B-chain. Most of the A-B chain
interactions involve charged side chains; six are buried salt bridges, and 10
are involved in interchain hydrogen bonds .In VMD I saw the two chains split up
at atime and then get together.I only know that I should write -merge in
pdb2gmx line.According to the informations above how can you help me?
1. pdb2gmx_mpi -f 1ppbfree.pdb -p 1ppbfree.top -o 1ppbfree.gro -merge
2.editconf_mpi -f 1ppbfree.gro -o -d 0.8 -bt octahedron
3. genbox_mpi -cp out.gro -cs -p 1ppbfree.top -o 1ppbfree-gen.gro
4. grompp_mpi -v -f 1ppbfree-en.mdp -c 1ppbfree-gen.gro -o
1ppbfree-en.tpr -p 1ppbfree.top
5.mdrun_mpi -v -s 1ppbfree-en.tpr -o 1ppbfree-en.trr -c 1ppbfree-aftermin.gro
-g 1ppbfree-en.log -e 1ppbfree-en.edr
---------------------------------
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