[gmx-users] (no subject)

Kingsley Theras Primus Dass . 105726107 at gms.tcu.edu.tw
Tue Nov 8 04:45:03 CET 2016

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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