<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman,new york,times,serif;font-size:12pt"><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;">A pair within the cutoff distance (e.g., 0.35nm) either belongs to $2 or $3, but cannot belong to both columns. <br>If the program finds a pair shorter than 0.35nm, and the angle is smaller than 30deg., then the program put this pair in the column 2.<br>If the program finds a pair shorter than 0.35nm, and the angle is larger than 30deg., then the program put this pair in the column 3.<br><br>Jianguo<br><br><br><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><font face="Tahoma" size="2"><hr size="1"><b><span style="font-weight: bold;">From:</span></b> ZHAO Lina <lnzhao99@gmail.com><br><b><span style="font-weight: bold;">To:</span></b> Discussion list for GROMACS users
<gmx-users@gromacs.org><br><b><span style="font-weight: bold;">Sent:</span></b> Wednesday, 16 March 2011 15:31:30<br><b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] Re: g_hbond output<br></font><br><meta http-equiv="x-dns-prefetch-control" content="off"><div class="gE iv gt"><table class="cf gJ" cellpadding="0"><tbody><tr><td class="gF gK"><table class="cf ix" cellpadding="0"><tbody><tr><td><div class="iw"><span class="lHQn1d"><img class=" f g8 " alt=""></span><span></span></div>
</td></tr></tbody></table></td><td class="gH"><br></td></tr><tr><td valign="top"><br></td><td valign="top"><br></td><td valign="top"><br></td></tr></tbody></table></div><div class="ii gt"><div> s0 legend "Hydrogen bonds"<br>
@ s1 legend "Pairs within 0.35 nm"<br> 0 0 0<br> 200 0 0<br> 400 2 1<br>
600 0 3<br> 800 0 2<br> 1000 1 0<br><br>Here is my question, since there is already one bond formed, then why there is none pairs in 1000?<br>
</div></div><br><br><div class="gmail_quote">On Wed, Mar 16, 2011 at 3:16 PM, Jianguo Li <span dir="ltr"><<a rel="nofollow" ymailto="mailto:ljggmx@yahoo.com.sg" target="_blank" href="mailto:ljggmx@yahoo.com.sg">ljggmx@yahoo.com.sg</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;">If I understand correctly, $2 is the number of hydrogen bonds defined by cutoff distance and the cutoff angle. $3 is the number of pairs within the cutoff distance, but beyond the cutoff angle. You may got different number of hbonds using different cutoff distance and cutoff angle.<br>
Jianguo<br><br><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><font face="Tahoma" size="2"><hr size="1"><b><span style="font-weight: bold;">From:</span></b> ZHAO Lina <<a rel="nofollow" ymailto="mailto:lnzhao99@gmail.com" target="_blank" href="mailto:lnzhao99@gmail.com">lnzhao99@gmail.com</a>><br>
<b><span style="font-weight: bold;">To:</span></b> Discussion list for GROMACS users <<a rel="nofollow" ymailto="mailto:gmx-users@gromacs.org" target="_blank" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br><b><span style="font-weight: bold;">Sent:</span></b> Wednesday, 16 March 2011
13:33:57<br><b><span style="font-weight: bold;">Subject:</span></b> [gmx-users] Re: g_hbond output<br></font><div><div></div><div class="h5"><br>@ legend length 2<br>@ s0 legend "Hydrogen bonds"<br>@ s1 legend "Pairs within 0.35 nm"<br>
0 0 0<br> 200 0 0<br> 400 2 1<br>
600 0 3<br> 800 0 2<br> 1000 1 0<br> :<br> 50000 3 2<br><br>Here the situations, what's the $2 and $3 mean, why when $1=1000, $3=0 if the $3 means pairs.<br>
<br>I tried pymol, and on the last frame,<br>there were 4 hydrogen bonds, between 7 residues. it's different from here 3 2<br><br>Thanks and sorry for last email without my realization it sent.<br><br>lina<br>
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