Hi,
I think I may have not understood you again, sorry. I think you're
asking if you can use two molecules as an anchor, right? If so that
cannot work; the way that autoimage works it can only use 1 molecule
as the anchor. That anchor should be the molecule that on average is
close to everything you want together in your system. By default
cpptraj chooses the first molecule, but as you've probably seen that's
not always the best choice. Most times which molecule the anchor
should be is clear, but you may need to experiment a bit to find out
which one looks the best to you.
Anyway, hope this clears things up - sorry for the confusion.
-Dan
On Wed, Jun 4, 2014 at 11:15 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> On Wed, Jun 4, 2014 at 9:43 AM, mish <smncbr.gmail.com> wrote:
>> Yes, they are two molecules in terms of they they are written in topology.
>> Residues 2-114 and 115-229 are two domains of a protein. I was not clear
>> enough in my previous email, probably.
>
> Actually, I think I wasn't clear enough. The reason I asked you to run
> the command 'molinfo !:WAT' (actually, even better would be 'molinfo
> :2-229') was to see how cpptraj thinks the molecule layout should be
> so I can start debugging. If CPPTRAJ thinks they are one molecule that
> may be an issue with how cpptraj is reading the topology, but if it
> thinks there are two molecules that is an issue with 'autoimage'
> itself. If you could provide me off-list with a topology and restart
> file so I can try and reproduce the problem that would be ideal.
>
> Also, what version of cpptraj are you using? If not V14 (from
> AmberTools 14) you should definitely upgrade.
>
> -Dan
>
>>
>> I want to know if it is possible to assign multimeric structure as anchor
>> residues or not (or can be only one as it is returned in the error) ?
>>
>> only autoimage followed by center the whole complex in the periodic cell
>> (image origin center) works fine.
>>
>> Thanks
>> Mish
>>
>>
>>
>> On Wed, Jun 4, 2014 at 4:26 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>>
>>> Hi,
>>>
>>> Are you sure residues 2-229 do not span two molecules in your
>>> topology? What is the output of 'molinfo !:WAT'?
>>>
>>> -Dan
>>>
>>> On Wed, Jun 4, 2014 at 9:11 AM, mish <smncbr.gmail.com> wrote:
>>> > I have a question related to autoimage task in cpptraj. I would like to
>>> > center complex (a ligand followed by a diamer protein in top file) during
>>> > imaging but assigning anchor to protein seems not work.
>>> > input file:
>>> > parm solvated.parm7
>>> > trajin traj1.dcd
>>> > autoimage anchor :2-229
>>> > trajout traj-imaged.nc netcdf
>>> >
>>> > .....................................................
>>> > ACTION SETUP FOR PARM 'solvated.parm7' (1 actions):
>>> > 0: [autoimage anchor :2-229]
>>> > Mask [:2-229] corresponds to 2 molecules
>>> > Error: Anchor mask [:2-229] corresponds to 2 mols, should only be 1.
>>> > ------------------------------------------------------------
>>> >
>>> > I think its taking both monomers as a molecules and generating error. I
>>> am
>>> > sure there will be some way to do it, but would I like to know if it can
>>> be
>>> > done using autoimage.
>>> >
>>> > Thanks
>>> > Mish
>>> > _______________________________________________
>>> > AMBER mailing list
>>> > AMBER.ambermd.org
>>> > http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>>
>>>
>>> --
>>> -------------------------
>>> Daniel R. Roe, PhD
>>> Department of Medicinal Chemistry
>>> University of Utah
>>> 30 South 2000 East, Room 201
>>> Salt Lake City, UT 84112-5820
>>> http://home.chpc.utah.edu/~cheatham/
>>> (801) 587-9652
>>> (801) 585-6208 (Fax)
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>> _______________________________________________
>> AMBER mailing list
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>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
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 Wed Jun 04 2014 - 11:00:06 PDT
