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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Received on Tue Feb 16 2016 - 10:30:03 PST
