Can you send me the necessary files off-list to try and reproduce this?
Also, what is your exact command in ParmEd? I've tested the use of CGenFF
atom types with ParmEd's chamber conversion and it works as expected, so
I'm not sure why you'd be getting this error...
HTH,
Jason
On Tue, Feb 16, 2016 at 1:02 PM, Amy Rice <arice3.hawk.iit.edu> wrote:
> Hi all,
> I am having problems trying to convert my psf/pdb combo (generated using
> vmd and psfgen) into a prmtop/crd using chamber within parmed.py. The
> problem seems to be that the atom types are not being read correctly from
> the psf. The error I'm getting says "Atom type C321 not present in AtomType
> list". I have double checked the psf, and it does not contain any atom type
> C321; it seems parmed is misreading the atom type CC321. This is only the
> 3rd atom in my psf, so I suspect it could have problems with some of the
> other longer atom types as well (such as CC3161, etc). I am using
> AmberTools 15.
>
> Does anyone have suggestions on how I can get around this problem?
> Thank you,
> - Amy
>
> --
> Amy Rice
> Ph.D. Student
> Physics Department
> Illinois Institute of Technology
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>
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Feb 16 2016 - 19:00:03 PST
