[gmx-users] Drude force field

[Justin Lemkul]

On 7/20/19 12:26 AM, Myunggi Yi wrote:
> Dear Justin,
>
> I've followed the instructions, and I prepared my system.
>
> I've got the following error message.
>
> " No default Bond types."
>
> There are several errors.
>
> The bond is between atoms 43 and 45, and the following is a part of the
> dmpc.itp, which is generated by pdb2gmx with drude-2013f_2018_10.ff
>
>      43     OD30CL      1   DMPC    O21     43     1.4847    15.5994   ;
> qtot 1.803
>      44       DRUD      1   DMPC   DO21     44    -1.4847          0   ;
> qtot 0.318
>      45        LPD      1   DMPC   LPMA     45      -0.17          0   ;
> qtot 0.148
>      46        LPD      1   DMPC   LPMB     46      -0.17          0   ;
> qtot -0.022
>      47     CD2O3B      1   DMPC    C21     47    2.72816     11.611   ;
> qtot 2.706
>      48       DRUD      1   DMPC   DC21     48   -2.03116          0   ;
> qtot 0.675
>
> It seems gromacs added a bond to them, which is not available in the
> dmpc.itp file.
> Is it common the bond between polar heavy atom and the lone pair virtual
> sites?

There should be no bonds to lone pairs. It seems there is an error in 
the .rtp entry for the lipid. The conversion script I used explicitly 
removes these but clearly there is some kind of bug that's not catching 
this. I will look into it. For now, simply remove any LP references in 
[bonds] and regenerate the topology.

> Program information:
> GROMACS:      gmx grompp, version 2016-dev-20181220-a2cab74
>
> Command line:
>    gmx grompp -f em.mdp -c ../gg.gro -r ../gg.gro -p ../topol.top -o em.tpr
>
>
> In addition, I do have not integer total charge.
>
> NOTE 2 [file topol.top, line 49]:
>    System has non-zero total charge: -0.000464
>
> Of course, when I generate the protein itp, the total charge was 0.00.
> As you know DMPC is neutral too.
> After combine protein, dmpc, water, this happened.

That's just rounding error. You're going to encounter this a lot due to 
the large number of fractionally charged particles in a polarizable system.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
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