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On 29/10/2011 9:47 PM, James Starlight wrote:
<blockquote
cite="mid:CAALQopxhuWH0K1U6=jbT9f3H-BEpca-eWMfVYq0=CpgW4oHNdA@mail.gmail.com"
type="cite">sure but I could not find possible parameter for
-scale option<br>
</blockquote>
<br>
Huh? What has scaling got to do with it?<br>
<br>
<blockquote
cite="mid:CAALQopxhuWH0K1U6=jbT9f3H-BEpca-eWMfVYq0=CpgW4oHNdA@mail.gmail.com"
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>
So align with X with -princ. Then in another call to editconf rotate
it to align with whatever you want.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAALQopxhuWH0K1U6=jbT9f3H-BEpca-eWMfVYq0=CpgW4oHNdA@mail.gmail.com"
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'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"><<a
moz-do-not-send="true" href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></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 7:38 PM, James Starlight
wrote:
<blockquote type="cite">Mark, hello!<br>
<br>
<br>
It's clear now about termii<br>
<br>
also I'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 class="h5"><br>
<br>
<blockquote type="cite"> <br>
James<br>
<br>
<div class="gmail_quote">2011/10/29 Mark Abraham <span
dir="ltr"><<a moz-do-not-send="true"
href="mailto:Mark.Abraham@anu.edu.au"
target="_blank">Mark.Abraham@anu.edu.au</a>></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'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'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'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'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'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>
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