[gmx-users] Help! A dummy atom definition problem!

[Wang Qin]

Hi Maik,
      I really did mix up a dummy atom with a virtual site. Any difference?
      Thank you very much for your help.

Regards,
Qin


On 9/12/07, Maik Goette <mgoette at mpi-bpc.mpg.de> wrote:
>
> The problem actually is, that you mixed up a dummy atom with a virtual
> site, I guess.
>
> Virtual sites are not allowed to have a mass, as the error message
> claims. Also, a proper hydrogen should have a mass.
>
> If you want a hydrogen to appear, you have to place a particle in
> A-state which has no non-bonded interaction, i.e. LJ & QQ interactions
> should be zero. If you want to prevent it from flying away, you should
> put bonded terms to the particle.
> In the B-state, the QQ and LJ should be there (whereas the LJ
> interaction for a hydrogen is 0 anyway).
>
> 21      opls_999        1       LG4     H21     21      0.0000  1.00800
>         opls_172        0.4650  1.00800
>
> opls_999   DUM   0     1.008000     0.000    A     0.000000   0.000000
>
> So, I expect, this is, how it should look like.
> Be aware of the missing bonded terms in the force field for a DUM
> particle. Maybe, you want to call it H instead...
>
> Regards
>
> Maik Goette, Dipl. Biol.
> Max Planck Institute for Biophysical Chemistry
> Theoretical & computational biophysics department
> Am Fassberg 11
> 37077 Goettingen
> Germany
> Tel.  : ++49 551 201 2310
> Fax   : ++49 551 201 2302
> Email : mgoette[at]mpi-bpc.mpg.de
>         mgoette2[at]gwdg.de
> WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/
>
>
> Wang Qin wrote:
> > Hi there,
> >        I met the problem when I ran "grompp", the errors are:
> > ERROR 1 [file "po4lig4tip3.top", line 26741]:
> >   virtual site H21 (Res LG4-173) has non-zero mass 1.008
> >        Check your topology.
> >
> > ERROR 2 [file "po4lig4tip3.top", line 26741]:
> >   virtual site H22 (Res LG4-173) has non-zero mass 1.008
> >        Check your topology.
> >
> >       Then I checked my topology file, here were the definition of
> > LG4-173 H21 and H22: ( I want to convert the dummy atoms to H atoms)
> >    ;nr          type    resnr   residue atom    cgnr    charge
> > mass            type_B  charge_B        mass_B
> > 21      opls_999        1       LG4     H21     21      0.0000
> > 1.00800         opls_172        0.4650  1.00800
> > 22      opls_999        1       LG4     H22     22      0.0000
> > 1.00800         opls_172        0.4650  1.00800
> >
> >        in which opls_999 was from what I defined by myself in the force
> > field itp file:
> > opls_999   DUM   0     1.008000     0.000    V     0.000000   0.000000
> >
> >       I changed the both of the mass_A to 0.00000, but that didn't help.
> >       Does anyone have ideas on that?
> >        Thank you very much.
> >
> > Regards,
> > Qin
> >
> >
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