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

[Wang Qin]

Thank you so much.

On 9/11/07, Yang Ye <leafyoung at yahoo.com> wrote:
>
> On 9/12/2007 12:39 AM, Wang Qin wrote:
> > 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?
> it's an H as long as it shares the same VDW as H and it carries the same
> charge as H.
> >      Thank you.
> >
> > Regards,
> > Qin
> >
> > On 9/11/07, *Yang Ye* <leafyoung at yahoo.com
> > <mailto: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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