<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40"><head><meta http-equiv=Content-Type content="text/html; charset=us-ascii"><meta name=Generator content="Microsoft Word 12 (filtered medium)"><style><!--
/* Font Definitions */
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0in;
margin-bottom:.0001pt;
font-size:11.0pt;
font-family:"Calibri","sans-serif";}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:purple;
text-decoration:underline;}
span.EmailStyle17
{mso-style-type:personal-compose;
font-family:"Calibri","sans-serif";
color:windowtext;
font-weight:normal;
font-style:normal;}
.MsoChpDefault
{mso-style-type:export-only;}
@page WordSection1
{size:8.5in 11.0in;
margin:1.0in 1.25in 1.0in 1.25in;}
div.WordSection1
{page:WordSection1;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]--></head><body lang=EN-US link=blue vlink=purple><div class=WordSection1><p class=MsoNormal>Hi,<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>The mechanism for specifying special bonds for the pdb2gmx program, using the specbond.dat file (manual section 5.6.7), seems to me not general enough. The characteristic length of the bond is specifiable, but the range of lengths for which a bond is assumed is hardcoded as +-10% of the characteristic length. I, for example, am perturbing structures using the Concoord method, and lengths of disulfide bonds sometimes vary by more than 10%.<o:p></o:p></p><p class=MsoNormal>I therefore suggest that two values would be added at the end of the line declaring a special bond, specifying the minimum and maximum lengths. These two values would be optional, so as not to break the existing arrangement, which would remain as the default. This should not require more than a few extra lines of code and would be, in my opinion, very useful.<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>What do you say?<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Thanks,<o:p></o:p></p><p class=MsoNormal>Ehud Schreiber.<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p></div></body></html>