sure but I could not find possible parameter for -scale option -[no]princ bool no Orient molecule(s) along their principal axes
from that I found that only yes\ no options is aviable for princ :( of course I could do the ssame via combination of the -align vector 0 0 0 Align to target vector -translate vector 0 0 0 Translation -rotate vector 0 0 0 Rotation around the X, Y and Z axes in degrees but this would require many calculations so I'm looking for most simplest way of orientation of my molecule along required coordinate 2011/10/29 Mark Abraham <[email protected]> > On 29/10/2011 7:38 PM, James Starlight wrote: > > 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? > > > Did you start by trying to look up the answer in editconf -h yourself? > > Mark > > > > 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 >> Please search the archive at >> 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 >> > > > > > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > 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 >
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