Justin, hello! I've desided to make simulation of my GA peptide under GROMOS96 53A6 force field extended with Berger lipids ( on analogy to KALP simulation because both of that lipids are membrane alpha helices with similar topology )
About termii- As I understood you've added ACE and NH2 termii to KALP via Amber tools software. I havent that software now but pdb2gmx under GROMOS96 53A6 force field may add only NH(2) cap to the C-end and COO(H) to the N-end instead of ACE and NH2. Identified residue VAL2 as a starting terminus. Identified residue TRP16 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully Select start terminus type for VAL-2 0: NH3+ 1: NH2 2: None It's not quite unferstand for me why pdb2gmx add the termii in such wrong manner ( e.g ACE and other groups also contains in the .rtp of this ff). Finally why I cant chose NH(2) for the last residue and the COOH for the first ? And what difference beetwen such termii specification would be as the consequence ? James
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