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

[Maik Goette]

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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