antechamber -i sustiva_new.pdb -fi pdb -o sustiva.mol2 -fo mol2 -c bcc -s 2
I am running antechamber. can the the command make the mol2 file a bit relaxed from pdb file?
Justin Lemkul
No, antechamber generates force field parameters, which can then be used in subsequent minimization and dynamics runs.
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Jamoliddin Razzokov
Actually I use the following command in order to equilibrate the system in Amber: sander -O -i $f.in -o $f.out -inf $f.inf -c 3roll.$l -ref 3roll.$l -r 3roll.$f -p 3roll.top -x 3roll$f.x -e 3roll$f.ene
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