Dear gmx-users, I'm trying to simulate a single protonated "Lysine" molecule in a water box using oplsaa force field. The molecular formular of the protonated Lysine molecule is (NH3+)CH(COO-)(CH2)4NH3+. To do it, I first obtained the initial atomic coordinates of Lysine from PRODRG website, then created conf.gro and topol.top files using pdb2gmx command. My conf.gro and the first part of the topol.top files are as following: ------------------------------------------------------------------------- 1. conf.gro Gromacs Runs One Microsecond At Cannonball Speeds 25 1LYSH N 1 -1.465 -0.606 -0.293 1LYSH H1 2 -1.546 -0.645 -0.249 1LYSH H2 3 -1.491 -0.524 -0.343 1LYSH H3 4 -1.426 -0.673 -0.356 1LYSH CA 5 -1.365 -0.571 -0.190 1LYSH HA 6 -1.407 -0.502 -0.131 1LYSH CB 7 -1.331 -0.694 -0.105 1LYSH HB1 8 -1.263 -0.667 -0.037 1LYSH HB2 9 -1.415 -0.723 -0.059 1LYSH CG 10 -1.275 -0.814 -0.182 1LYSH HG1 11 -1.344 -0.845 -0.248 1LYSH HG2 12 -1.193 -0.785 -0.231 1LYSH CD 13 -1.238 -0.932 -0.092 1LYSH HD1 14 -1.315 -0.950 -0.030 1LYSH HD2 15 -1.222 -1.012 -0.150 1LYSH CE 16 -1.112 -0.905 -0.008 1LYSH HE1 17 -1.033 -0.888 -0.068 1LYSH HE2 18 -1.126 -0.826 0.052 1LYSH NZ 19 -1.083 -1.022 0.076 1LYSH HZ1 20 -1.001 -1.004 0.131 1LYSH HZ2 21 -1.160 -1.039 0.137 1LYSH HZ3 22 -1.068 -1.102 0.018 1LYSH C 23 -1.240 -0.510 -0.256 1LYSH O1 24 -1.241 -0.498 -0.392 1LYSH O2 25 -1.139 -0.473 -0.173 0.54461 0.62928 0.52832 --------------------------------------------------------------------- 2. topol.top #include "ffoplsaa.itp" [ moleculetype ] ; Name nrexcl Protein 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1 opls_287 1 LYSH N 1 -0.3 14.0067 ; qtot -0.3 2 opls_290 1 LYSH H1 1 0.33 1.008 ; qtot 0.03 3 opls_290 1 LYSH H2 1 0.33 1.008 ; qtot 0.36 4 opls_290 1 LYSH H3 1 0.33 1.008 ; qtot 0.69 5 opls_283 1 LYSH CA 1 0.04 12.011 ; qtot 0.73 6 opls_140 1 LYSH HA 1 0.06 1.008 ; qtot 0.79 7 opls_136 1 LYSH CB 2 -0.12 12.011 ; qtot 0.67 8 opls_140 1 LYSH HB1 2 0.06 1.008 ; qtot 0.73 9 opls_140 1 LYSH HB2 2 0.06 1.008 ; qtot 0.79 10 opls_136 1 LYSH CG 3 -0.12 12.011 ; qtot 0.67 11 opls_140 1 LYSH HG1 3 0.06 1.008 ; qtot 0.73 12 opls_140 1 LYSH HG2 3 0.06 1.008 ; qtot 0.79 13 opls_136 1 LYSH CD 4 -0.12 12.011 ; qtot 0.67 14 opls_140 1 LYSH HD1 4 0.06 1.008 ; qtot 0.73 15 opls_140 1 LYSH HD2 4 0.06 1.008 ; qtot 0.79 16 opls_292 1 LYSH CE 5 0.19 12.011 ; qtot 0.98 17 opls_140 1 LYSH HE1 5 0.06 1.008 ; qtot 1.04 18 opls_140 1 LYSH HE2 5 0.06 1.008 ; qtot 1.1 19 opls_287 1 LYSH NZ 6 -0.3 14.0067 ; qtot 0.8 20 opls_290 1 LYSH HZ1 6 0.33 1.008 ; qtot 1.13 21 opls_290 1 LYSH HZ2 6 0.33 1.008 ; qtot 1.46 22 opls_290 1 LYSH HZ3 6 0.33 1.008 ; qtot 1.79 23 opls_271 1 LYSH C 7 0.7 12.011 ; qtot 2.49 24 opls_272 1 LYSH O1 7 -0.8 15.9994 ; qtot 1.69 25 opls_272 1 LYSH O2 7 -0.8 15.9994 ; qtot 0.89 ----------------------------------------------------------------------------------------- My question is... why is the total charge (qtot) of the molecule 0.89 as shown in topol.top above, instead of the expected +1? The gomacs automatically choose opls_283 (atom number 5 in topol.top above) as C-alpha (CA), instead of opls_224B, the usual C-alpha for amino acids. If I manually replace CA from opls_283 (charge=0.04) to opls-224B (charge=0.14), then the total charge improves to be 0.99. Is this the correct way to fix the problem of non-integer total charge in this case? If so, is 0.99 for total charge close enough to 1 so I can move on to the next stage? I greatly appreciate in advance your kind help and/or advice! Regards, Sung Hyun