[gmx-users] Drude force field

Sat Jul 20 06:27:23 CEST 2019

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?

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.

Any suggestion?

Thank you.

On Thu, Jul 18, 2019 at 11:22 AM Justin Lemkul <jalemkul at vt.edu> wrote:

> On Wed, Jul 17, 2019 at 8:58 PM Myunggi Yi <myunggi at pukyong.ac.kr> wrote:
>
> > Thank you Dr. Lemkel,
> >
> > I don't have ions in my simulation. It's a neutral system with a protein
> in
> > membrane bilayer with solvent.
> > I have downloaded the force field (Drude FF for charmm FF in Gromacs
> > format). to run the simulation with charmm FF in "Gromacs 2019.3".
> > However, it seems the format of the file does not match with the current
> > version.
> >
> > In the web,
> >
> > Compile and install as you would any other (post-5.0) GROMACS version. If
> > you attempt to use *ANY OTHER VERSION OF GROMACS, the Drude features will
> > not be accessible.*
> >
> > There are 5.0 and 5.1 series of Gromacs versions. Which one should I use?
> >
> > Or, it there a way to modify the force field format to use the current
> > version of Gromacs?, Then I will modify the format.
> >
> >
> Read the information at the previous link more carefully. You cannot use
> any released version of GROMACS. You must use the developmental version as
> instructed in that link.
>
> -Justin
>
>
> >
> > On Thu, Jul 18, 2019 at 9:43 AM Justin Lemkul <jalemkul at vt.edu> wrote:
> >
> > >
> > >
> > > On 7/17/19 8:39 PM, Myunggi Yi wrote:
> > > > Dear users,
> > > >
> > > > I want to run a simulation with a polarizable force field.
> > > >
> > > > How and where can I get Drude force field for the current version of
> > > > Gromacs?
> > >
> > > Everything you need to know:
> > >
> > > http://mackerell.umaryland.edu/charmm_drude_ff.shtml
> > >
> > > The implementation is not complete. If your system has ions, do not use
> > > GROMACS due to the lack of NBTHOLE. In that case, use NAMD, CHARMM, or
> > > OpenMM. The Drude model is still considered experimental, hence it is
> > > not officially supported yet. There have been a lot of snags along the
> > > way (mostly in my time to get the code up to par for official
> inclusion).
> > >
> > > -Justin
> > >
> > > --
> > > ==================================================
> > >
> > > Justin A. Lemkul, Ph.D.
> > > Assistant Professor
> > > Office: 301 Fralin Hall
> > > Lab: 303 Engel Hall
> > >
> > > Virginia Tech Department of Biochemistry
> > > 340 West Campus Dr.
> > > Blacksburg, VA 24061
> > >
> > > jalemkul at vt.edu | (540) 231-3129
> > > http://www.thelemkullab.com
> > >
> > > ==================================================
> > >
> > > --
> > > Gromacs Users mailing list
> > >
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> --
>
> ==========================================
>
> Justin A. Lemkul, Ph.D.
>
> Assistant Professor
>
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
>
> ==========================================
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