[gmx-users] (no subject)
ddhecnu at gmail.com
Tue Nov 8 07:40:04 CET 2016
If your residue contains new atom types, you should add them to the
atomtypes.atp and ffnonbonded.itp files.
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:
> 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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