[gmx-users] adding mix solvent

[Nur Syafiqah Abdul Ghani]

Dear All,

I already produce my co-solvent topology file also with gro file.
Next step is i need to put the co-solvent first before i enter the
water molecule inside my box and mix them with the protein.
But right now i had a problem during put the co-solvent part.

I used this command : genbox -cp protein_box.gro -ci solv.gro -p
control.top -o protein_solv.gro

but then there was no any molecule of my co-solvent inside the box
with the protein.
Then i know i must have the itp file to include in the control topology.
But what i can do with the topology of the co-solvent?What is the
relationship between co-solvent.gro and
co-solvent.top which i  might can used both of them in my GROMACS simulation?

Four your infomation i used antechamber to produced my co-solvent topology.
Any advises from the pro one?

Thanks in advance!

-- 
Best Regards,

Nur Syafiqah Abdul Ghani,
Theoretical and Computational Chemistry Laboratory,
Department of Chemistry,
Faculty of Science,
Universiti Putra Malaysia,
43400 Serdang,
Selangor.
013-7188131
alternative email : syafiqahabdulghani at gmail.com