sure but I could not find possible parameter for -scale option<br><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>
<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 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></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 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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</blockquote>
</div>
<br>
<br>
<fieldset></fieldset>
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</blockquote>
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