[gmx-users] (no subject)

[Dd H]

If your residue contains new atom types, you should add them to the
atomtypes.atp and ffnonbonded.itp files.

Dading Huang

On 8 November 2016 at 11:44, Kingsley Theras Primus Dass . <
105726107 at gms.tcu.edu.tw> wrote:

> Hello users!!
>
> I generated a Topology file for SO3- using ATB topology generator , which
> is compatible with GROMACS. Then I copied the .rtp file from ATB and pasted
> it into  GROMACS aminoacid.rtp.
>
>  The  partial charge of aminoacid sulfated-tyrosine was -1.
> When I run -pdb2gmx there was error saying the atoms were missing ,
> -------------------------------------------------------
> Program gmx pdb2gmx, VERSION 5.1
> Source code file:
> /home/hsulab00/Documents/gromacs-5.1/src/gromacs/
> gmxpreprocess/pdb2top.cpp,
> line: 1584
>
> Fatal error:
> There were 6 missing atoms in molecule Protein_chain_D, if you want to use
> this incomplete topology anyhow, use the option -missing
>
>
> then I ran pdb2gmx -ignh -p topol.top -missing
>
> It generated the topology file. But the parital charge of sulfated tyrosine
> was changed to -2, coz of missing hydrogen atoms.
>
> can you please suggest some solutions , to overcome this problem.
>
>
>
>
> Thank You
> --
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