[gmx-users] how are you

james zhang james.zhangj at gmail.com
Thu Nov 1 05:32:57 CET 2007

Hi, Dr. Liang
Please use PRODRG server.

or you can write some script to convert Material studio pdb file to PDB bank

On 10/31/07, zhuliang at tju.edu.cn <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. 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.
>     At the same time, how to obtain the parameter of tobramycin in gmx
> opls
> format?
>     Thank you and I am looking forward to hearing from you soon!
> Best wishes
> zhuliang
> ------------------------------
> Dr.Liang Zhu
> Department of Chemical Engineering
> School of Chemical Engineering and Technology
> Tianjin University Tianjin, 300072 P. R. China
> Tel: +86-22-27405754 Fax:+86-22-27374971
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Sincerely yours,
James Jianzhang
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