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

[Wang Qin]

Hi Yang,
     I was thinking to set mass_B to 0 but what I was supposed to do is
converting dummy atoms to H atoms. In my opinion, it wouldn't be H atoms if
I set the mass to 0. Am I thinking wrong?
     Thank you.

Regards,
Qin

On 9/11/07, Yang Ye <leafyoung at yahoo.com> wrote:
>
> you have set the mass_B to 0 as well.
>
> On 9/11/2007 10:54 PM, 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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