Hi,
The 'center' command will not perform any alignment beyond
translation, but I think that should be enough since I don't think
LEaP will do any rotation of coordinates (others please correct me if
I'm wrong here). The alignment will use whatever mask you give it, so
if you specify ':1' it will center residue 1 in your input trajectory
on residue in the reference, etc.
-Dan
On Thu, Jun 23, 2016 at 5:49 PM, Sushil Mishra <sushilbioinfo.gmail.com> wrote:
> 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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>> AMBER mailing list
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
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 Fri Jun 24 2016 - 11:00:03 PDT
