<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div><meta http-equiv="content-type" content="text/html; charset=utf-8"><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></body></html>