From: Kenno Vanommeslaeghe (kvanomme_at_rx.umaryland.edu)
Date: Fri Jul 25 2014 - 16:44:15 CDT
On 07/25/2014 04:30 PM, Cenk Denktas wrote:
> /FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR C NH3 (ATOMS 105 107)/
The definitions of these two atom types essentially preclude them from
being bonded to one another, so something must have gone horribly wrong in
your psf generation.
> /anybody know how to solve this problem?//
Yes, generate a correct psf.
> /I use the par_all27_prot_lipid.inp file /
Although this has probably nothing to do with your problem, be advised
there exists a CHARMM36 force field that has significant improvements. It
can be downloaded with one click at:
http://mackerell.umaryland.edu/charmm_ff.shtml#charmm
and there are some NAMD usage instructions at
http://mackerell.umaryland.edu/~kenno/cgenff/program.html#namd
(just omit the line that says "parameters molecule.str")
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