<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body text="#000000" bgcolor="#FFFFFF">
On 2/11/2011 8:32 AM, Olivia Waring wrote:
<blockquote
cite="mid:CABXeruyEX6x6MBT5XsRPo0S5QPdy2SxnCF-QtVSpOUhOCzbFeg@mail.gmail.com"
type="cite"><span class="Apple-style-span" style="color: rgb(51,
51, 51); font-family: arial,sans-serif; font-size: 13px;
background-color: rgb(255, 255, 255);">
<div><span style="color: rgb(51, 51, 51); font-family: arial,
sans-serif; font-size: 13px; background-color: rgb(255, 255,
255); ">Dear Gromacs users,</span></div>
<span style="color: rgb(51, 51, 51); font-family:
arial,sans-serif; font-size: 13px; background-color: rgb(255,
255, 255);">
<div><span style="color: rgb(51, 51, 51); font-family: arial,
sans-serif; font-size: 13px; background-color: rgb(255,
255, 255); "><br>
</span></div>
First of all, many thanks to Justin for his assistance with my
previous question.
<div><br>
</div>
<div>I have defined a new residue type in the oplsaa force
field, changing the aminoacids.rtp file accordingly. pdb2gmx
worked just fine; but when I try to preprocess, I get the
following output: </div>
<div><br>
</div>
<div>
<div>WARNING 1 [file ffbonded.itp, line 58]:</div>
</div>
</span></span></blockquote>
<br>
You'll need to inspect at and before this line in this file to
diagnose.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CABXeruyEX6x6MBT5XsRPo0S5QPdy2SxnCF-QtVSpOUhOCzbFeg@mail.gmail.com"
type="cite"><span class="Apple-style-span" style="color: rgb(51,
51, 51); font-family: arial, sans-serif; font-size: 13px;
background-color: rgb(255, 255, 255); "><span style="color:
rgb(51, 51, 51); font-family: arial, sans-serif; font-size:
13px; background-color: rgb(255, 255, 255); ">
<div>
<div> Overriding Bond parameters.</div>
<div><br>
</div>
<div> old: 0.1229 476976 0.1229 476976</div>
<div> new: C O 1 0.13270 179075.2</div>
<div><br>
</div>
<div><br>
</div>
<div>WARNING 2 [file ffbonded.itp, line 64]:</div>
<div> Overriding Bond parameters.</div>
<div><br>
</div>
<div> old: 0.1522 265266 0.1522 265266</div>
<div> new: C CT 1 0.14950 265265.6</div>
<div><br>
</div>
<div><br>
</div>
<div>WARNING 3 [file ffbonded.itp, line 67]:</div>
<div> Overriding Bond parameters.</div>
<div><br>
</div>
<div> old: 0.149 334720 0.149 334720</div>
<div> new: CA C 1 0.14240 392459.2</div>
<div><br>
</div>
<div><br>
</div>
<div>WARNING 4 [file ffbonded.itp, line 73]:</div>
<div> Overriding Bond parameters.</div>
<div><br>
</div>
<div> old: 0.1419 374050 0.1419 374050</div>
<div> new: C CB 1 0.14240 392459.2</div>
<div><br>
</div>
<div><br>
</div>
<div>-------------------------------------------------------</div>
<div>Program grompp, VERSION 4.5.4</div>
<div>Source code file: topdirs.c, line: 76</div>
<div><br>
</div>
<div>Fatal error:</div>
<div>Invalid bond type 0</div>
<div>For more information and tips for troubleshooting,
please check the GROMACS</div>
<div>website at <a moz-do-not-send="true"
href="http://www.gromacs.org/Documentation/Errors"
target="_blank" style="color: rgb(61, 84, 89); ">http://www.gromacs.org/Documentation/Errors</a></div>
</div>
<div><br>
</div>
<div><br>
</div>
<div>The error is rather cryptic, and I'm having trouble
tracking it down... I even went to the source code
(topdirs.c), but I'm still not sure where exactly this
"invalid bond type" is being defined. </div>
<div><br>
</div>
<div>Thank you so much for your help,</div>
<div>Olivia</div>
</span></span><br clear="all">
<div><br>
</div>
-- <br>
<div>Olivia Waring (王维娅)</div>
<div>Princeton University '12</div>
<div>AB Chemistry</div>
<br>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
</blockquote>
<br>
</body>
</html>