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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