[gmx-users] how are you

[Mark Abraham]

zhuliang at tju.edu.cn wrote:
> Sir:
>     How are you! I am a new user of gmx.At first,sincere tribute to you and all
> the gmx developers!
>     I want to perform a molecular dynamics simulation on the tobramycin aqueous
> soluton by gmx. On the simulation process,I encounter some problem and I can't
> treat  with it by myself and I hope you will give me a hand.
>     Tobramycin is a aminoglycosidic substance, Its pdb file is not availabe in the
> PDB bank, so I generate it with a comercial software Material studio. but it is
> not in consistent with gmx command of pdb2gmx.

More information is needed in order to actually help you.

> I want to know how can I deal with
> it and it the other way to generate a pdb file of tobramycin in gmx format.

Well-formed PDB *is* accepted by GROMACS.

>     At the same time, how to obtain the parameter of tobramycin in gmx opls
> format?

Start at the beginning... see 
http://wiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation

Mark