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Hi,<br>
<br>
Yes, this was done on purpose to reflect the different use of charge
groups in CHARMM and GROMACS. Check out the mailing list archives
for more details about this. <br>
<br>
On another note you might like to take a look at the contributed
CHARMM36 force field (available to download on the GROMACS website).
There is a DPPG entry in the lipids.rtp file that should help in
making a CHARMM27 DPPG rtp entry (if you wish to use the CHARMM27
lipids rather than the CHARMM36 ones).<br>
<br>
Cheers<br>
<br>
Tom <br>
<br>
On 06/08/11 00:22, Michael McGovern wrote:
<blockquote
cite="mid:1312586522.17308.YahooMailNeo@web65708.mail.ac4.yahoo.com"
type="cite">
<div style="color: rgb(0, 0, 0); background-color: rgb(255, 255,
255); font-family: times new roman,new york,times,serif;
font-size: 12pt;">
<div>
<meta http-equiv="content-type" content="text/html;
charset=ISO-8859-1">
<div style="font-family: times,serif; font-size: 12pt;">Hi,
I'm making a lipid topology for DPPG in the charmm
forcefield in gromacs 4.5. I'm putting it together from
pieces of what already exists as suggested in the charmm
files. I noticed that there are charge groups in the
original charmm files, and these were reflected in the
gromacs topology in the 4.5 beta release, but in 4.5.3 and
4.5.4, every atom has its own charge group. </div>
<div style="font-family: times,serif; font-size: 12pt;"><br>
</div>
<div style="font-family: times,serif; font-size: 12pt;">So for
instace, POPC in the beta release had a topology that began:</div>
<div>
<div><font class="yiv910318136Apple-style-span" face="'times
new roman', 'new york', times, serif">[ POPC ]</font></div>
<div><font class="yiv910318136Apple-style-span" face="'times
new roman', 'new york', times, serif"> [ atoms ]</font></div>
<div><font class="yiv910318136Apple-style-span" face="'times
new roman', 'new york', times, serif"> N
NTL -0.60 0</font></div>
<div><font class="yiv910318136Apple-style-span" face="'times
new roman', 'new york', times, serif"> C11
CTL2 -0.10 0</font></div>
<div><font class="yiv910318136Apple-style-span" face="'times
new roman', 'new york', times, serif"> C12
CTL5 -0.35 0</font></div>
<div><font class="yiv910318136Apple-style-span" face="'times
new roman', 'new york', times, serif"> C13
CTL5 -0.35 0</font></div>
<div><font class="yiv910318136Apple-style-span" face="'times
new roman', 'new york', times, serif"> C14
CTL5 -0.35 0</font></div>
<div><font class="yiv910318136Apple-style-span" face="'times
new roman', 'new york', times, serif"> H11 HL
0.25 0</font></div>
<div><font class="yiv910318136Apple-style-span" face="'times
new roman', 'new york', times, serif"> H12 HL
0.25 0</font></div>
<div><font class="yiv910318136Apple-style-span" face="'times
new roman', 'new york', times, serif"> H21 HL
0.25 0</font></div>
<div><font class="yiv910318136Apple-style-span" face="'times
new roman', 'new york', times, serif"> H22 HL
0.25 0</font></div>
<div><font class="yiv910318136Apple-style-span" face="'times
new roman', 'new york', times, serif"> H23 HL
0.25 0</font></div>
<div><font class="yiv910318136Apple-style-span" face="'times
new roman', 'new york', times, serif"> H31 HL
0.25 0</font></div>
<div><font class="yiv910318136Apple-style-span" face="'times
new roman', 'new york', times, serif"> H32 HL
0.25 0</font></div>
<div><font class="yiv910318136Apple-style-span" face="'times
new roman', 'new york', times, serif"> H33 HL
0.25 0</font></div>
<div><font class="yiv910318136Apple-style-span" face="'times
new roman', 'new york', times, serif"> H41 HL
0.25 0</font></div>
<div><font class="yiv910318136Apple-style-span" face="'times
new roman', 'new york', times, serif"> H42 HL
0.25 0</font></div>
<div><font class="yiv910318136Apple-style-span" face="'times
new roman', 'new york', times, serif"> H43 HL
0.25 0</font></div>
<div><font class="yiv910318136Apple-style-span" face="'times
new roman', 'new york', times, serif"> C15
CTL2 -0.08 1</font></div>
<div><font class="yiv910318136Apple-style-span" face="'times
new roman', 'new york', times, serif"> H51
HAL2 0.09 1</font></div>
<div><font class="yiv910318136Apple-style-span" face="'times
new roman', 'new york', times, serif"> H52
HAL2 0.09 1</font></div>
<div><font class="yiv910318136Apple-style-span" face="'times
new roman', 'new york', times, serif"> P1 PL
1.50 2</font></div>
<div><font class="yiv910318136Apple-style-span" face="'times
new roman', 'new york', times, serif"> O3
O2L -0.78 2</font></div>
<div><font class="yiv910318136Apple-style-span" face="'times
new roman', 'new york', times, serif"> O4
O2L -0.78 2</font></div>
<div><font class="yiv910318136Apple-style-span" face="'times
new roman', 'new york', times, serif"> O1
OSL -0.57 2</font></div>
<div><font class="yiv910318136Apple-style-span" face="'times
new roman', 'new york', times, serif"> O2
OSL -0.57 2</font></div>
<div><font class="yiv910318136Apple-style-span" face="'times
new roman', 'new york', times, serif"> C1
CTL2 -0.08 3</font></div>
<div style="font-family: times,serif; font-size: 12pt;">...</div>
<div style="font-family: times,serif; font-size: 12pt;">While
in 4.5.4 this is</div>
<div>
<div><font class="yiv910318136Apple-style-span"
face="'times new roman', 'new york', times, serif">[
POPC ]</font></div>
<div><font class="yiv910318136Apple-style-span"
face="'times new roman', 'new york', times, serif"> [
atoms ]</font></div>
<div><font class="yiv910318136Apple-style-span"
face="'times new roman', 'new york', times, serif">
N NTL -0.60 0</font></div>
<div><font class="yiv910318136Apple-style-span"
face="'times new roman', 'new york', times, serif">
C11 CTL2 -0.10 1</font></div>
<div><font class="yiv910318136Apple-style-span"
face="'times new roman', 'new york', times, serif">
C12 CTL5 -0.35 2</font></div>
<div><font class="yiv910318136Apple-style-span"
face="'times new roman', 'new york', times, serif">
C13 CTL5 -0.35 3</font></div>
<div><font class="yiv910318136Apple-style-span"
face="'times new roman', 'new york', times, serif">
C14 CTL5 -0.35 4</font></div>
<div><font class="yiv910318136Apple-style-span"
face="'times new roman', 'new york', times, serif">
H11 HL 0.25 5</font></div>
<div><font class="yiv910318136Apple-style-span"
face="'times new roman', 'new york', times, serif">
H12 HL 0.25 6</font></div>
<div><font class="yiv910318136Apple-style-span"
face="'times new roman', 'new york', times, serif">
H21 HL 0.25 7</font></div>
<div><font class="yiv910318136Apple-style-span"
face="'times new roman', 'new york', times, serif">
H22 HL 0.25 8</font></div>
<div><font class="yiv910318136Apple-style-span"
face="'times new roman', 'new york', times, serif">
H23 HL 0.25 9</font></div>
<div><font class="yiv910318136Apple-style-span"
face="'times new roman', 'new york', times, serif">
H31 HL 0.25 10</font></div>
<div><font class="yiv910318136Apple-style-span"
face="'times new roman', 'new york', times, serif">
H32 HL 0.25 11</font></div>
<div><font class="yiv910318136Apple-style-span"
face="'times new roman', 'new york', times, serif">
H33 HL 0.25 12</font></div>
<div><font class="yiv910318136Apple-style-span"
face="'times new roman', 'new york', times, serif">
H41 HL 0.25 13</font></div>
<div><font class="yiv910318136Apple-style-span"
face="'times new roman', 'new york', times, serif">
H42 HL 0.25 14</font></div>
<div><font class="yiv910318136Apple-style-span"
face="'times new roman', 'new york', times, serif">
H43 HL 0.25 15</font></div>
<div><font class="yiv910318136Apple-style-span"
face="'times new roman', 'new york', times, serif">
C15 CTL2 -0.08 16</font></div>
<div><font class="yiv910318136Apple-style-span"
face="'times new roman', 'new york', times, serif">
H51 HAL2 0.09 17</font></div>
<div style="font-family: times,serif; font-size: 12pt;">...</div>
<div style="font-family: times,serif; font-size: 12pt;">The
charge groups do not have integer charge and are all one
atom. The beta version has groups that agree with the
charmm groups and have integer charge. Was this changed
on purpose? The beta version seems correct to me, but am
I missing something as to why this change would be made?
</div>
<div style="font-family: times,serif; font-size: 12pt;">Thanks</div>
</div>
</div>
</div>
</div>
</blockquote>
<br>
<pre class="moz-signature" cols="72">--
Dr Thomas Piggot
University of Southampton, UK.
</pre>
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