On Fri, Jun 10, 2016, Sushil Mishra wrote:
>
> 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.
It looks like you are correct: the "nocenter" option seems to be active with
"set x box" but not with "solvateBox". Do you have a need for such behavior?
It looks a bit tricky to implement.
...dac
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Received on Wed Jun 22 2016 - 20:30:02 PDT
