Hi gmx users!
I've created the topology of a peptide using pdb2gmx(4.0-rc4) converting
aromatic rings into virtual sites. I've used the grompp(4.0_rc4) to compile the
input for the mdrun and it was ok, no error message, but when running
mdrun(4.0-rc4):
Program mdrun4, VERSION 4.0_rc4
Source code file: vsite.c, line: 1504
Fatal error:
Virtual site atom 29 is part of a charge group of only virtual sites, but its
first constructing atom (26) is part of a different charge group, this
combination is not allowed.
I've repeated the process using grompp(3.3), mdrun(3.3) and the same topology
(it was created by pdb2gmx(4.0-rc4)) and the simulation run well.
What could I do? I'd like enjoy the new implementations in PME from gromacs
4.0! ;)
A little part from my topology:
23 N 3 TRP N 12 -0.28 15.0147
24 H 3 TRP H 12 0.28 0
25 CH1 3 TRP CA 13 0 13.019
26 MW 3 TRP MW1 14 0 52.0557
27 MW 3 TRP MW2 14 0 64.087
28 CH2 3 TRP CB 15 0 14.027
29 CB 3 TRP CG 16 -0.14 0
30 CR5 3 TRP CD1 16 -0.14 0
31 HCR 3 TRP HD1 16 0.14 0
32 CB 3 TRP CD2 16 0 0
33 NR5* 3 TRP NE1 16 -0.05 0
34 H 3 TRP HE1 16 0.19 0
35 CB 3 TRP CE2 17 0 0
36 CR6 3 TRP CE3 18 -0.14 0
37 HCR 3 TRP HE3 18 0.14 0
38 CR6 3 TRP CZ2 19 -0.14 0
39 HCR 3 TRP HZ2 19 0.14 0
40 CR6 3 TRP CZ3 20 -0.14 0
41 HCR 3 TRP HZ3 20 0.14 0
42 CR6 3 TRP CH2 21 -0.14 0
43 HCR 3 TRP HH2 21 0.14 0
44 C 3 TRP C 22 0.38 12.011
45 O 3 TRP O 22 -0.38 15.9994
Novos endereços, o Yahoo! que você conhece. Crie um email novo com a sua
cara @ymail.com ou @rocketmail.com.
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