On Mon, Apr 27, 2015 at 11:31 AM, CHAMI F. <fatima.chami.durham.ac.uk> wrote:
> if the "principal" command is omitted and the command
> "vector vx principal x" is run in cpptraj, I still get a vector
> what kind of vector is this since it is different to the principal axis
'vector principal x' will output the principal axis with the largest
eigenvalue. In Cartesian space there are three principal axes. The
axis ordering is X > Y > Z for historical reasons (i.e. because that
is the way it was in PTRAJ).
-Dan
>
> many thanks
> Fatima
>
> ________________________________________
> From: Daniel Roe [daniel.r.roe.gmail.com]
> Sent: Monday, April 27, 2015 4:36 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] cpptraj V14.25 issues with old Amber topology files (Amber 11)
>
> In order to construct the vector pseudo trajectory, cpptraj creates a
> matching topology where the vector origin (OXYZ) is "bonded" to the vector
> head (VXYZ). The internal routines automatically try to guess at what this
> bond length should be based on the name, which is what generates the
> warning. So you can safely ignore the warning, but of course do *not* try
> to use this topology for any kind of simulation!
>
> -Dan
>
> On Monday, April 27, 2015, CHAMI F. <fatima.chami.durham.ac.uk> wrote:
>
>> Dear all,
>>
>> I used cpptraj in AmberTools 14 to get principal axis and a pseudo
>> trajectory of the vector. I get warning messages in cpptraj and cpptraj
>> processing complete without any errors..
>> do I need to convert the old topology file and if so what is the utility
>> code to use
>>
>> ACTION OUTPUT:
>> Warning: Could not determine atomic number from name [VXYZ]
>> Warning: : Determining default bond distances from element types.
>> Warning: Bond length not found for ?? - O, using default= 1.600000
>> Writing topology 0 () to 'px-rot.prmtop' with format Amber Topology
>> Writing 'px-rot.mdcrd' as Amber Trajectory
>>
>> -------------------------------------------------------------------------------------
>> my cpptraj input is:
>> parm ../myos_stripwat-4anew4.prmtop
>> trajin ../myos_wat-4anew4_md3-8.mdcrd 1 10 1
>> principal :1-155 dorotation out eigen-rot.dat
>> trajout myos-rot.mdcrd
>> vector v1 :1-155 principal x out vector_PX-rot.dat
>> vector v2 :1-155 principal x trajout px-rot.mdcrd parmout px-rot.prmtop
>>
>> many thanks
>> Fatima
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> 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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Received on Mon Apr 27 2015 - 11:00:04 PDT
