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>
<br>James<br><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 class="im">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>
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I can't understand any of that :)<div class="im"><br>
<br>
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<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>
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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 class="im">
<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>
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Because they've either not been parameterized, coded or tested.<div class="im"><br>
<br>
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And what difference beetwen such termii specification would be as the consequence ?<br>
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<br></div><font color="#888888">
Mark</font><div><div></div><div class="h5"><br>
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