[gmx-users] vsites, ffamber, charge groups, N-terminus, and crashes
Jochen Hub
jochen at xray.bmc.uu.se
Wed Sep 30 16:12:23 CEST 2009
Hi Berk,
thanks a lot for the quick response. Please let me know if you require a
topology/mdp-file/starting structure of the crashing simulation.
Concerning pdb2gmx, there is however and issue with the charge group
assignments. In my ffamber99sb.rtp, the H's in the N-terminal are set
into *separate* charge groups:
[ NASN ]
[ atoms ]
N amber99_39 0.18010 1
H1 amber99_17 0.19210 2 <-- !
H2 amber99_17 0.19210 3 <-- !
H3 amber99_17 0.19210 4 <-- !
CA amber99_11 0.03680 5
In the generated topology, however, the H are merged into the same CG
(but not together with the nitrogen):
; nr type resnr residue atom cgnr charge mass t
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
8 amber99_28 1 NASN HA 4 0.1231 0 ;
qtot 0.9163
That does not happen at the lysines. Is there a specific reason why
pdb2gmx "overrules" the parameters in the rtp file (only at the
terminus)? (By the way, the charge group generation at the terminus is
not affected by vsites, the H's are in the same CG also without vsites.)
I feel that even if separate charge groups for each atom is not the
gromacs philosophy, pdb2gmx should stick to the rtp file, shouldn't it?
Best,
Jochen
Berk Hess wrote:
> Hi,
>
> There are two separate issues here.
>
> One is the charge groups assignment with AMBER.
> I think that in Gromacs we, in general, do not want all atoms in
> separate charge groups,
> but we want to include at least the hydrogens in a charge group with
> the heavy atom.
> We would also like the option to make every atom a single charge group,
> but pdb2gmx of 4.1 already has an option for this.
> Since the AMBER force fields are currently not in the Gromacs package,
> we don't have control over the charge group assignment.
>
> The second issue is the crashing of the simulations.
> I don't see why simulations would crash with the slightly strange
> charge group assignment.
> But it sounds like there is a bug somewhere.
> I suspect it could happen when an NH3 group is partially over a box edge.
> This is strange though, since I think I check all nasty combinations
> of vsite generation
> and charge groups.
>
> I already got such a file from Bert.
>
> Berk
>
> > Date: Wed, 30 Sep 2009 15:35:42 +0200
> > From: jochen at xray.bmc.uu.se
> > To: gmx-users at gromacs.org
> > Subject: [gmx-users] vsites, ffamber, charge groups, N-terminus, and
> crashes
> >
> > 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
> >
> >
> > --
> > ---------------------------------------------------
> > 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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--
---------------------------------------------------
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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