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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>>
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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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Received on Thu Jun 23 2016 - 08:30:02 PDT
