From: Tim Isgro (timisgro_at_ks.uiuc.edu)
Date: Thu Mar 04 2004 - 13:56:44 CST
Your protein has proline as the first residue in each segment. Because of
proline's funny cyclic geometry, you need to patch those N-termini with
the PROP patch in the topology file (psfgen: first PROP). Without the
patch, those first nitrogens are of type NH3, which yielded your original
problem. The attched psfgen script works.
Also, the script you sent me explicitly patched the N and C termini (first
NTER; last CTER). Note that psfgen does this automatically for the first
and last protein residues in a segment. Finally, you should also use
alias ILE CD1 CD.
On Tue, 2 Mar 2004, Tim Isgro wrote:
> Hi Han,
> There are no parameters for a CP3-NH3 bond in the Charmm parameter files.
> Do the peptide segments contain any exotic residues for which parameters
> might not be defined?
> On Tue, 2 Mar 2004, Han Choe wrote:
> > Dear All,
> > I generated a PSF file of 4 peptide segments using VMD and ran a
> > molecular dynamics simulation using NAMD. But I got an error message,
> > read "CAN'T FIND BOND PARAMETERS FOR BOND CP3-NH3 IN PARAMETER FILES".
> > What'd be wrong?
> > Cheers,
> > Han
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