[gmx-users] SEP and HO atom type - again

[Luciane Vieira de Mello]

Dear Anton,

Sorry for taking too much of your time. But I am getting confused with
Gromos and Gromacs forcefield.
As you probably followed in gmx-l, I managed to solve the atom type
problem. But I am facing the mass problem again.

[phospho]$ grompp -p topol_withGAD.top -c
conf_GAD.gro -f em.mdp
                         :-)  G  R  O  M  A  C  S  (-:


WARNING 2 [file "topol_withGAD.top", line 31434]:
  atom O1 (Res GAD-512) has mass 0

WARNING 3 [file "topol_withGAD.top", line 31434]:
  atom C1 (Res GAD-512) has mass 0

WARNING 4 [file "topol_withGAD.top", line 31434]:
  atom O2 (Res GAD-512) has mass 0

WARNING 5 [file "topol_withGAD.top", line 31434]:
  atom C2 (Res GAD-512) has mass 0

WARNING 6 [file "topol_withGAD.top", line 31434]:
  atom O1P (Res GAD-512) has mass 0

WARNING 7 [file "topol_withGAD.top", line 31434]:
  atom HAB (Res GAD-512) has mass 0


The masses are not defined in the .itp file for gromacs. Can I add them to
it?

Thanks in advance,
Luciane


> Yes: for the Gromos forcefield (ffG43*) the masses of atoms are defined
> in the .rtp entries, or in the molecule topologies themselves. For the
> Gromacs forcefields (ffgmx*), they are defined for the atom types.
> Still, Gromacs expects a mass field in the atom type definition, so they
> are set to 0 (for the ffG43*nb.itp)
>
>
> --
> Groetjes,
>
> Anton
>   ________ ___________________________________________________________
> |        | Anton Feenstra                                            |
> | .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
> | |----  | De Boelelaan 1083 - 1081 HV Amsterdam - The Netherlands   |
> | |----  | Tel: +31 20 44 47608 - Fax: +31 20 44 47610               |
> | ' __   | Feenstra at chem.vu.nl - http://www.chem.vu.nl/afdelingen/FAR|
> |  /  \  |-----------------------------------------------------------|
> | (    ) | Dept. of Biophysical Chemistry - University of Groningen  |
> |  \__/  | Nijenborgh 4 - 9747 AG Groningen - The Netherlands        |
> |   __   | Tel +31 50 363 4327 - Fax +31 50 363 4800                 |
> |  /  \  | K.A.Feenstra at chem.rug.nl - http://md.chem.rug.nl/~anton   |
> | (    ) |-----------------------------------------------------------|
> |  \__/  | "If You See Me Getting High, Knock Me Down"               |
> |        | (Red Hot Chili Peppers)                                   |
> |________|___________________________________________________________|
>
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