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
>> > _______________________________________________
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>> > 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
>>
> _______________________________________________
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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 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 - 10:30:02 PDT
