[AMBER] How to move the protein to the corner of the box.

From: Parviz Seifpanahi Shabane <sparviz.vt.edu>
Date: Sat, 19 Aug 2017 16:49:37 -0400

Dear AMBER User,
I want to move my protein to the corner of the box to make it smaller, I am
interested dynamics of just one part of the proteins and I will put
restoration another part on a fix in the corner, I used the "translate"
command but it seems it does not work. any suggestions? this my leap script
source leaprc.ff10
set default PBradii bondi
mods = loadAmberParams frcmod.opc
mods = loadAmberParams frcmod.ionsjc_tip4pew
mol = loadpdb 1kx5__1_mutation_tail_slice.pdb
addions mol Na+ 0
addions mol Cl- 0

#addions2 mol Na+ 26
#addions2 mol Cl- 26

solvateBox mol OPCBOX 4 iso
translate mol {3 3 0}
saveamberparm mol H4-DNA-OPC-FF10-mutated-position.top

Best Regards
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Received on Sat Aug 19 2017 - 14:00:03 PDT
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