Many thanks. I was just curious if I am not doing any mistake. I needed it
for TI calculations in *pmemed* where I thought to keep coordinates of
non-TI atoms atoms in wildtype and mutant unchanged. But there was an easy
workaround, and I had translated coordinates of all the mutants with
respect to wild-type generated by by *tLeap*.
Best,
Sushil
On Thu, Jun 23, 2016 at 12:22 PM, David A Case <david.case.rutgers.edu>
wrote:
> 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 - 22:00:02 PDT
