<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)">
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