[gmx-users] GTG to GAG with amber FF99SB force field

[yaolisha at msu.edu]

Dear Gromacs users: I use gromacs.4-5-3 to calculate the free energy changes for the GTG to GAG alchemy process, where charge annihilation is performed first followed by soft core VDW calculation. When doing the soft core VDW calculation, I see this error message ?Fatal error: [ file gtg_vdw.top, line 314 ]: Proper Dih. multiplicity can not be perturbed 1.000000!=3.000000?.Line 314 has the following content ?17    16    18    24     9?The atoms with VDW radius and well depth changes include 20         CT      3    THR    CG2     20    -0.0000      12.01   CTD  0.0  12.01 ; qtot 0.0439 21         HC      3    THR   HG21     21     0.0000      1.008   HCD  0.0  1.008; qtot 0.1081 22         HC      3    THR   HG22     22     0.0000      1.008   HCD  0.0  1.008; qtot 0.1723 23         HC      3    THR   HG23     23     0.0000      1.008   HCD  0.0  1.008; qtot 0.2365 24         OH      3    THR    OG1     24    -0.0000         16   OHD   0.0  16   ; qtot -0.4396 25         HO      3    THR    HG1     25     0.0000      1.008   HOD  0.0  1.008; qtot -0.0294Atom types CTD, HCD, OHD, HOD are defined in a separate file and included in the topology file. My question is how to solve this problem and a related question is whether the overall setup is correct.Best, Lishan
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