[gmx-users] Regarding preparation of .itp file for a new molecule

Mark Abraham mark.abraham at anu.edu.au
Wed Sep 27 02:09:07 CEST 2006

> Hai all...
>            I am a newbie to gromacs simulation software and its file
> formats. I want to develop coarse grain models for surfactant systems by
> using atomistic simulations. I got a .pdb file for BTMAC surfactant.
>           But to run simuations on gromacs,I need to include .itp file in
> source code. Can anyone of u tell me,Is it difficult to prepare a .itp
> file
> for a new molecule?? If it is so, I want to know how many days it will
> take
> to prepare....... And also Please tell suggestions to prepare a .itp file
> for a new molecule....

It is tedious but not difficult to prepare an .itp file description of a
molecule. Please read chapters 4 and 5 of the manual. Consider using the
PRODRG server, and/or the pdb2gmx tool.


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