[gmx-users] posre.itp

Mark Abraham Mark.Abraham at anu.edu.au
Mon Nov 10 07:21:11 CET 2008

Bhawana Gupta wrote:
> hello everyone,
> Pls tell me from where i can get posre.itp means format of this file.

Chapter 5 of the manual, like I said last time. Repeating the same 
questions doesn't help you look like someone worth donating time to 
helping :-)

> Here in one mail named topology, you had given solution for making pdb 
> file from one other than PRODRG i.e.
>  Build a small one by hand in a text editor (making sure the density is
> suitable and there won't be steric clashes across periodic boundaries),
> replicate it with genbox, and equilibrate.
> But sorry i didnot get it. So explain it by another way.

Please do not combine threads. This makes it hard for people to follow 

I'm sorry you don't understand my instructions, but they are perfectly 
clear, and will work if you understand the file format you are creating. 
Unfortunately, nobody has yet managed to write a software package that 
can already do everything every user might want. Since, ionic liquids 
are outside the normal scope of GROMACS, it's not surprising that there 
is not immediate support for it. It would also be a poor idea for 
someone new to GROMACS to immediately try to do things outside of its 
normal scope - the learning curve would be very steep indeed.

If by "ionic liquids" you mean "aqueous solutions containing ions", then 
that's another matter.

> can we use PRODRG for making peptides with usual amino acid.

Yes, caveat all the normal warnings about PRODRG.


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