[gmx-users] vsite problem in gromacs 4.0

[zazeri]

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(3.3.1), mdrun(3.3.1) 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! Any suggestion would be appreciated, thanks. Fernando "Zazeri" Lopes.


A little part from my topology (as GROMOS87):
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



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