Hi,
You can not do much.
The reason for this error message is also valid for older versions.
It can not be guaranteed that the virtual sites in one charge group will
have the same periodic shift. But before 4.0 there was no check for this.
I would simply not use vsite aromatics. I am in favor of completely
removing this option from pdb2gmx, since you do not gain so much
compared with dt=4 or 5 fs with -vsite h (and optionally heavy hydrogens).
If you really want to use the vsite aromatics, you can put all atoms
in the aromatic groups in separate charge groups, but that will make
the simulation slightly slower.
Berk
> Date: Tue, 4 Nov 2008 02:45:13 -0800
> From: [EMAIL PROTECTED]
> To: [email protected]
> Subject: [gmx-users] vsite problem in gromacs 4.0
>
> 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
>
>
>
> Novos endereços, o Yahoo! que você conhece. Crie um email novo com a
> sua cara @ymail.com ou @rocketmail.com.
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