Amber99sb-ildn ff with Hydroxyproline

User discussions
1

I am working on type 3 collagen with hyp residues.
1 N HYP A 2
2 HN1 HYP A 2
3 HN2 HYP A 2
4 CD HYP A 2
5 HD1 HYP A 2
6 HD2 HYP A 2
7 CA HYP A 2
8 HA HYP A 2
9 CB HYP A 2
10 HB1 HYP A 2
11 HB2 HYP A 2
12 CG HYP A 2
13 HG HYP A 2
14 OD1 HYP A 2
15 HE HYP A 2
16 C HYP A 2
17 O HYP A 2

when I add this with amber99sb-ildn ff, I got and error .
‘Fatal error:

There is a dangling bond at at least one of the terminal ends and the force

field does not provide terminal entries or files. Fix your terminal residues

so that they match the residue database (.rtp) entries, or provide terminal

database entries (.tdb).‘

help me to add hyp parameters correctly to my ff

2

Have you tried using the CHARMM36m forcefield instead? My understanding is that amber99sb-ildn has some issues dealing with collagen