Thanks a lot for the new information. Does this feature align mol.rst over
reference structure (all/nonH/backbone atoms ?) or it copies exact
coordinates of the common part from reference structure and images rest of
the part ? I just want to understand if tiMerge would never fail if I am
using this procedure to generate start and end states for TI calculation.
Best,
Sushil
On Fri, Jun 24, 2016 at 12:09 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> FYI cpptraj now has the ability to center coordinates on a reference
> structure. For example, if you wanted to shift your system back to
> your reference system:
>
> parm mol.parm7
> trajin mol.rst7
> parm system.pdb
> reference system.pdb parm system.pdb
> center <mask> reference
> image !(<mask>)
>
> Where <mask> is the atom mask selecting the molecule you want centered.
>
> -Dan
>
>
> On Wed, Jun 22, 2016 at 10:58 PM, Sushil Mishra <sushilbioinfo.gmail.com>
> wrote:
> > 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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> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> > _______________________________________________
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>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
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>
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Received on Thu Jun 23 2016 - 17:00:03 PDT
