[gmx-users] coordinate files for molecules consisting of new (non-standard) residues

Mark Abraham mark.abraham at anu.edu.au
Sat Nov 10 02:07:17 CET 2007

> Dear gromacs users,
> I am trying to set up a system with new (non-standard) residue blocks to
> study polymers and polymer-protein conjugates; however we will not have
> pdb
> files of molecules that we want to study.

Jumping straight in the deep end is a recipe for frustration. Make sure
you do some tutorial material, and get some practice setting up systems
where you haven't needed to use self-made residue blocks (if you haven't
already). You will need a thorough knowledge of Chapter 5 of the manual.

>  Is there a way of generating coordinate files and other necessary Gromacs
> files using only a sequence of these novel residues instead of the using
> pdb
> file and pdb2gmx?

No, there is no way within GROMACS to generate coordinates of any
structure, apart from adding hydrogens, and such tweaks. The wiki is
currently short of recommendations for molecule builders. Can people
please suggest some?


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