Sorry Daniel you are right. I thought I was using an updated installation.
Best,
Jesper
On Sep 16, 2013, at 7:31 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> What version of cpptraj are you using? This issue should have been
> fixed as of version 13.10.
>
> -Dan
>
> On Mon, Sep 16, 2013 at 1:23 AM, Sorensen, Jesper <jesorensen.ucsd.edu> wrote:
>> Hello,
>>
>> I ran a cpptraj calculation today and for the jcoupling keyword it seems it doesn't stick to the mask specified.
>>
>> jcoupling :1-15 outfile jcoupling.out
>>
>>
>> See abbreviated output here below.
>>
>>> 58: [jcoupling :1-15 outfile jcoupling.out]
>>> Warning: Jcoupling::setup: Karplus parameters not found for residue [25:GLY ]
>>> Warning: Jcoupling::setup: Karplus parameters not found for residue [266:Mg+ ]
>>> Warning: Jcoupling::setup: Karplus parameters not found for residue [268:Na+ ]
>>> Warning: Jcoupling::setup: Karplus parameters not found for residue [269:Cl- ]
>>> Warning: Jcoupling::setup: Karplus parameters not found for residue [270:Na+ ]
>>> Warning: Jcoupling::setup: Karplus parameters not found for residue [271:Cl- ]
>>> Warning: Jcoupling::setup: Karplus parameters not found for residue [272:Na+ ]
>>> J-COUPLING: [:1-15] Will calculate J-coupling for 120 dihedrals.
>>
>> I am thinking this is a bug. It is not critical since it still calculates the jcoupling parameters for the residues I want and actually only selects the correct 120 dihedrals. It just seems strange that it checks for Karplus parameters for residues I haven't selected.
>>
>> Best,
>> Jesper
>>
>>
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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
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>
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Received on Mon Sep 16 2013 - 09:00:04 PDT
