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

[Yang Ye]

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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