[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.
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
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