Hi, Dr. Liang<br>Please use PRODRG server.<br><a href="http://davapc1.bioch.dundee.ac.uk/programs/prodrg/">http://davapc1.bioch.dundee.ac.uk/programs/prodrg/</a><br><br>or you can write some script to convert Material studio pdb file to PDB bank format.
<br>Thanks.<br><br><div><span class="gmail_quote">On 10/31/07, <b class="gmail_sendername"><a href="mailto:zhuliang@tju.edu.cn">zhuliang@tju.edu.cn</a></b> <<a href="mailto:zhuliang@tju.edu.cn">zhuliang@tju.edu.cn</a>> wrote:
</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Sir:<br> How are you! I am a new user of gmx.At first,sincere tribute to you and all
<br>the gmx developers!<br> I want to perform a molecular dynamics simulation on the tobramycin aqueous<br>soluton by gmx. On the simulation process,I encounter some problem and I can't<br>treat with it by myself and I hope you will give me a hand.
<br> Tobramycin is a aminoglycosidic substance, Its pdb file is not availabe in the<br>PDB bank, so I generate it with a comercial software Material studio. but it is<br>not in consistent with gmx command of pdb2gmx. I want to know how can I deal with
<br>it and it the other way to generate a pdb file of tobramycin in gmx format.<br> At the same time, how to obtain the parameter of tobramycin in gmx opls<br>format?<br> Thank you and I am looking forward to hearing from you soon!
<br><br>Best wishes<br>zhuliang<br><br><br><br><br>------------------------------<br>Dr.Liang Zhu<br>Department of Chemical Engineering<br>School of Chemical Engineering and Technology<br>Tianjin University Tianjin, 300072 P. R. China
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</a><br></blockquote></div><br><br clear="all"><br>-- <br>Sincerely yours,<br>James Jianzhang<br><br>