Mark, hello!
It's clear now about termii also I'd like to know about orientation of my protein along specific axis e.g editconf -princ orient my protein along X but what should i do to orient it along other axis? James 2011/10/29 Mark Abraham <[email protected]> > On 29/10/2011 6:34 PM, James Starlight wrote: > >> 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. >> > > I can't understand any of that :) > > > >> 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). >> > > Termini are added by pdb2gmx using the terminus databases in the .n.tdb and > .c.tdb files, as you would know from your reading of chapter 5 of the manual > :-) Only things that are found there can be added by pdb2gmx - and not > everything you can imagine will be found there. If you want (for example) an > ACE group at your N-terminus, you need to build it using some other tool, > and arrange for the .rtp entry for ACE to exist (which it already does). > > > Finally why I cant chose NH(2) for the last residue and the COOH for the >> first ? >> > > Because they've either not been parameterized, coded or tested. > > > And what difference beetwen such termii specification would be as the >> consequence ? >> > > Mark > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to [email protected]. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >
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