<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body text="#000000" bgcolor="#FFFFFF">
<div class="moz-cite-prefix">Hi,<br>
<br>
This looks mainly like a bug, but could also partially be a
feature.<br>
In practice most force fields have atom types with unique masses,
so it doesn't matter.<br>
But this format currently gives the false impression that you
could change the mass.<br>
<br>
Could you file a redmine issue?<br>
<br>
Cheers,<br>
<br>
Berk<br>
<br>
On 03/21/2013 05:24 PM, Wouter Boomsma wrote:<br>
</div>
<blockquote
cite="mid:CAPU6s5TNmM_xuQ4aFAW6Oi0at5sJ3Wj64PzN7NjSL5zZuShaZQ@mail.gmail.com"
type="cite">
<meta http-equiv="Content-Type" content="text/html;
charset=ISO-8859-1">
<div>Hi,</div>
<div><br>
</div>
<div>I'm in the process of implementing a parser for gromacs
topology </div>
<div>files, and have a question about the aminoacids.n.tdb and </div>
<div>aminoacids.c.tdb type files. In the Gromacs parser, it seems </div>
<div>that when specifying a rule like this:</div>
<div><br>
</div>
<div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px
0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">[
NH3+ ]<br>
[ replace ]<br>
N N NH3 14.0027 -0.3<br>
CA CA CT1 12.011 0.21<br>
HA HA HB 1.008 0.10<br>
[ Add ]<br>
3 4 H N CA C<br>
HC 1.008 0.33 -1<br>
[ delete ]<br>
HN</blockquote>
</div>
<div><br>
</div>
<div>The mass specification - for instance the 14.0027, is not</div>
<div>used in the generation of the topology file, in contrast to</div>
<div>the charge value. I'm a little uncertain whether this is a</div>
<div>feature or a bug. Does anyone have any insight in this</div>
<div>matter?</div>
<div><br>
</div>
<div>Code wise, the responsible lines are in the pdb2top.c file, </div>
<div>in the name2type function:</div>
<div><br>
</div>
<div>
<div> at->atom[i].type =
restp[resind].atom[j].type;</div>
<div> at->atom[i].q = restp[resind].atom[j].q;</div>
<div> at->atom[i].m =
get_atomtype_massA(restp[resind].atom[j].type,</div>
<div> atype);</div>
</div>
<div><br>
</div>
<div>At this point in the code restp[resind].atom[j].m actually</div>
<div>contains the modified mass, but this is not copied to the</div>
<div>"at" object, which is later written to the topology file. </div>
<div><br>
</div>
<div>Thanks,</div>
<div>Wouter</div>
<div><br>
</div>
<br clear="all">
<div><br>
</div>
<div
style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)"></div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
</blockquote>
<br>
</body>
</html>