[AMBER] Unchanged coordinates in leap

From: mish <smncbr.gmail.com>
Date: Tue, 21 Jul 2015 11:13:07 +0200

Dear all,

I would like to know if there is some way to keep protein coordinates
unchanged when adding water box in tleap (in AmberTools 15). "set default
nocenter on" works fine when I am not adding any water box (coordinates of
complex.pdb written by tleap are unchanged). However, if I use SolvateBox
or SolvateOct, leap changes protein coordinates slightly. Am I missing
something or this how it should work ? My script looks like:

tleap -f - <<EOF

# load the AMBER force fields
source leaprc.ff14SB
loadAmberParams frcmod.ionsjc_tip3p

mol = protein-wt.pdb

set default nocenter on

solvateBox mol TIP3PBOX 11.0 0.75
savepdb mol complex.pdb


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Received on Tue Jul 21 2015 - 02:30:04 PDT
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