Yes I&#39;ve tried this way but obtained wrong result ;o<br><br>e.g after align along X I&#39;ve tried rotate along Z on 90 to obtain align on Z<br>-rotate 0 0 90<br><br>but I&#39;ve obtained structure aligned on Y :DD<br>
<br>Whta I&#39;ve done wrong?<br><br>James<br><br><div class="gmail_quote">2011/10/29 Mark Abraham <span dir="ltr">&lt;<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>&gt;</span><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">

  
    
  
  <div bgcolor="#FFFFFF" text="#000000"><div class="im">
    On 29/10/2011 9:47 PM, James Starlight wrote:
    <blockquote type="cite">sure but I could not find possible parameter for
      -scale option<br>
    </blockquote>
    <br></div>
    Huh? What has scaling got to do with it?<div class="im"><br>
    <br>
    <blockquote type="cite"><br>
      -[no]princ   bool   no      Orient molecule(s) along their
      principal axes<br>
      <br>
      from that I found that only yes\ no options is aviable for princ
      :(<br>
    </blockquote>
    <br></div>
    So align with X with -princ. Then in another call to editconf rotate
    it to align with whatever you want.<br><font color="#888888">
    <br>
    Mark</font><div><div></div><div class="h5"><br>
    <br>
    <blockquote type="cite">
      <br>
      of course I could do the ssame via combination of the <br>
      -align       vector 0 0 0   Align to target vector<br>
      -translate   vector 0 0 0   Translation<br>
      -rotate      vector 0 0 0   Rotation around the X, Y and Z axes in
      degrees<br>
      <br>
      but this would require many calculations so I&#39;m looking for most
      simplest way of orientation of my molecule along required
      coordinate<br>
      <div class="gmail_quote">2011/10/29 Mark Abraham <span dir="ltr">&lt;<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>&gt;</span><br>
        <blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
          <div bgcolor="#FFFFFF" text="#000000">
            <div> On 29/10/2011 7:38 PM, James Starlight
              wrote:
              <blockquote type="cite">Mark, hello!<br>
                <br>
                <br>
                It&#39;s clear now about termii<br>
                <br>
                also I&#39;d like to know about orientation of my protein
                along specific axis<br>
                <br>
                e.g editconf -princ orient my protein along X but what
                should i do to orient it along other axis?<br>
              </blockquote>
              <br>
            </div>
            Did you start by trying to look up the answer in editconf -h
            yourself?<br>
            <font color="#888888"> <br>
              Mark</font>
            <div>
              <div><br>
                <br>
                <blockquote type="cite"> <br>
                  James<br>
                  <br>
                  <div class="gmail_quote">2011/10/29 Mark Abraham <span dir="ltr">&lt;<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>&gt;</span><br>
                    <blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
                      <div>On 29/10/2011 6:34 PM, James Starlight wrote:<br>
                        <blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"> Justin, hello!<br>
                          <br>
                          I&#39;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 )<br>
                          <br>
                          About termii- As I understood you&#39;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.<br>
                        </blockquote>
                        <br>
                      </div>
                      I can&#39;t understand any of that :)
                      <div><br>
                        <br>
                        <blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"> <br>
                          Identified residue VAL2 as a starting
                          terminus.<br>
                          Identified residue TRP16 as a ending terminus.<br>
                          8 out of 8 lines of specbond.dat converted
                          successfully<br>
                          Select start terminus type for VAL-2<br>
                           0: NH3+<br>
                           1: NH2<br>
                           2: None<br>
                          <br>
                          It&#39;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).<br>
                        </blockquote>
                        <br>
                      </div>
                      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).
                      <div> <br>
                        <br>
                        <blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"> Finally why I cant chose NH(2) for the
                          last residue and the COOH for the first ?<br>
                        </blockquote>
                        <br>
                      </div>
                      Because they&#39;ve either not been parameterized,
                      coded or tested.
                      <div><br>
                        <br>
                        <blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"> And what difference beetwen such termii
                          specification would be as the consequence ?<br>
                        </blockquote>
                        <br>
                      </div>
                      <font color="#888888"> Mark</font>
                      <div>
                        <div><br>
                          -- <br>
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