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.
So for instace, POPC in the beta release had a topology that began:
[ POPC ]
[ atoms ]
N NTL -0.60 0
C11 CTL2 -0.10 0
C12 CTL5 -0.35 0
C13 CTL5 -0.35 0
C14 CTL5 -0.35 0
H11 HL 0.25 0
H12 HL 0.25 0
H21 HL 0.25 0
H22 HL 0.25 0
H23 HL 0.25 0
H31 HL 0.25 0
H32 HL 0.25 0
H33 HL 0.25 0
H41 HL 0.25 0
H42 HL 0.25 0
H43 HL 0.25 0
C15 CTL2 -0.08 1
H51 HAL2 0.09 1
H52 HAL2 0.09 1
P1 PL 1.50 2
O3 O2L -0.78 2
O4 O2L -0.78 2
O1 OSL -0.57 2
O2 OSL -0.57 2
C1 CTL2 -0.08 3
...
While in 4.5.4 this is
[ POPC ]
[ atoms ]
N NTL -0.60 0
C11 CTL2 -0.10 1
C12 CTL5 -0.35 2
C13 CTL5 -0.35 3
C14 CTL5 -0.35 4
H11 HL 0.25 5
H12 HL 0.25 6
H21 HL 0.25 7
H22 HL 0.25 8
H23 HL 0.25 9
H31 HL 0.25 10
H32 HL 0.25 11
H33 HL 0.25 12
H41 HL 0.25 13
H42 HL 0.25 14
H43 HL 0.25 15
C15 CTL2 -0.08 16
H51 HAL2 0.09 17
...
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?
Thanks
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