In (more) defense of Dan, Amber atom names follow the PDB standard for standard residues. So cpptraj should work with any amber system or any other program that adheres to the closest thing we have to a "standard" in the field. [1]
All the best,
Jason
[1] a notable exception is the handling of different tautomers, protomers, and protonation states. But the PDB standard applies the same residue names for each one...
> On Jun 4, 2014, at 3:11 PM, Geoffrey Gray <gmgray2.mail.usf.edu> wrote:
>
> Awesome, thanks, Dan!
>
> Geoffrey
>
>
>> On Wed, Jun 4, 2014 at 3:06 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>>
>> On Wed, Jun 4, 2014 at 9:38 AM, Geoffrey Gray <gmgray2.mail.usf.edu>
>> wrote:
>>> Error: Ref Atom [C7 ] not found in NA base [THY ]
>>>
>>> This is due to the fact that C7 in the Amber force field is C5M in the
>>> charmm force field.
>>
>> Yikes - this is an unfortunate result of my lack of experience with
>> charmm. Right now the atom names for the NA bases are hard-coded at
>> the top of the file
>> $AMBERHOME/AmberTools/src/cpptraj/src/AxisType.cpp. I eventually need
>> to make it so you can load up a custom reference, but for now the
>> workaround is to change the atom name for that base in AxisType.cpp
>> and recompile. However, I would do this in a separate directory so
>> that you don't accidentally lose anything. I'm attaching a version of
>> AxisType.cpp where I have made this modification so you can see what I
>> mean.
>>
>> Thanks for the report!
>>
>> -Dan
>>
>>>
>>> How can I fix this? I tried playing around with resmap, but this was
>>> unsuccessful.
>>>
>>> My script is
>>>
>>> ###
>>> parm dcd/dna.psf
>>> trajin dcd/merged-dna.dcd dcd
>>>
>>> nastruct naout na.dat resrange :3-33
>>> ###
>>>
>>>
>>> Thanks
>>>
>>> Geoffrey
>>> _______________________________________________
>>> 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)
>>
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--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Jun 04 2014 - 13:00:02 PDT
