Yes I've tried this way but obtained wrong result ;o e.g after align along X I've tried rotate along Z on 90 to obtain align on Z -rotate 0 0 90
but I've obtained structure aligned on Y :DD Whta I've done wrong? James 2011/10/29 Mark Abraham <[email protected]> > On 29/10/2011 9:47 PM, James Starlight wrote: > > sure but I could not find possible parameter for -scale option > > > Huh? What has scaling got to do with it? > > > > -[no]princ bool no Orient molecule(s) along their principal axes > > from that I found that only yes\ no options is aviable for princ :( > > > So align with X with -princ. Then in another call to editconf rotate it to > align with whatever you want. > > Mark > > > > 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 >> > > > > > > -- > 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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