[gmx-users] vsites, ffamber, charge groups, N-terminus, and crashes

[Jochen Hub]

Hi,

I have been trying to use vsites with AMBER99SB, but the simulation 
frequently cashes after a few hundred ps with the suspects (lincs 
warnings, 1-4 distance error). I could pinpoint the problem to erroneous 
charge group assignments generated by pdb2gmx at the NH3 group at the 
N-terminus. The following charge group assignments caused the error:

;   nr       type  resnr residue  atom   cgnr     charge       mass 
     1       MNH3      1   NASN    MN1      1          0      8.517   ; 
qtot 0
     2       MNH3      1   NASN    MN2      1          0      8.517   ; 
qtot 0
     3 amber99_39      1   NASN      N      1     0.1801          0   ; 
qtot 0.1801
     4 amber99_17      1   NASN     H1      2     0.1921          0   ; 
qtot 0.3722
     5 amber99_17      1   NASN     H2      2     0.1921          0   ; 
qtot 0.5643
     6 amber99_17      1   NASN     H3      2     0.1921          0   ; 
qtot 0.7564
     7 amber99_11      1   NASN     CA      3     0.0368     13.018   ; 
qtot 0.7932
...

The NH3 groups in the lysines were fine and did not cause any error. The 
only difference compared to the N-terminus is that each of the three H 
in the NH3 has its own charge group, but the vsites and the N are still 
in the same CG:

    30 amber99_11      2    LYP     CE     29    -0.0143     14.026   ; 
qtot 0.9937
    31 amber99_28      2    LYP    HE1     30     0.1135          0   ; 
qtot 1.107
    32 amber99_28      2    LYP    HE2     31     0.1135          0   ; 
qtot 1.221
    33       MNH3      2    LYP   MNZ1     32          0      8.517   ; 
qtot 1.221
    34       MNH3      2    LYP   MNZ2     32          0      8.517   ; 
qtot 1.221
    35 amber99_39      2    LYP     NZ     32    -0.3854          0   ; 
qtot 0.8353
    36 amber99_17      2    LYP    HZ1     33       0.34          0   ; 
qtot 1.175
    37 amber99_17      2    LYP    HZ2     34       0.34          0   ; 
qtot 1.515
    38 amber99_17      2    LYP    HZ3     35       0.34          0   ; 
qtot 1.855

Alternatively, I have also tried to give every single atom (including 
the vsites MN??) a separate charge group, which also worked fine.

1)
So, is there any reason why the dummies should be in the same CG as the 
nitrogen? Or should it be fine just to assign a separate CG to every atom?

2)
Is a bug report appreciated on that issue?

Best,

Jochen


-- 
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Dr. Jochen Hub
Molecular Biophysics group
Dept. of Cell & Molecular Biology
Uppsala University. Box 596, 75124 Uppsala, Sweden.
Phone: +46-18-4714451 Fax: +46-18-511755
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