Hello everyone:
I am using following keywords in tLeap (Amber16):
source leaprc.protein.ff14SB
source leaprc.gaff
source leaprc.water.tip3p
loadAmberParams frcmod.ionsjc_tip3p
m1 = loadpdb system.pdb
set default nocenter on
solvateBox m1 TIP3PBOX 13
saveamberparm m1 mol.parm7 mol.rst7
Why the coordinates of the protein in mol.rst7 are shifted after adding
waterbox ? I am using VMD to visualize mol.rst7 and system.pdb. If I do not
add solvent, it works as expected.
Sincerely,
Sushil
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Received on Fri Jun 10 2016 - 00:00:02 PDT
