Hi, Dr. Liang Please use PRODRG server. http://davapc1.bioch.dundee.ac.uk/programs/prodrg/
or you can write some script to convert Material studio pdb file to PDB bank format. Thanks. On 10/31/07, [EMAIL PROTECTED] <[EMAIL PROTECTED]> 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 > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Sincerely yours, James Jianzhang
_______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
