[gmx-users] making topology file for infinite crystal

Mark Abraham Mark.Abraham at anu.edu.au
Sun Feb 7 10:54:01 CET 2010

On 07/02/10 14:52, Vishal Agarwal wrote:
> Dear All,
> Can anyone help me how can I go about preparing the topology file for an
> infinite crystal of cellulose. I have prepared the .gro file for 5X5X5
> unit cells of cellulose II using GROMACS utility and intend to apply
> periodic BC on it. It has a glucose molecule as building block (GCLA).
> When I try running pdbgmx, I get an error for extra hydrogens (which is
> not there in itp file but is actually there in the original structure
> which I am using) and missing oxygen (-O).

People who might help aren't at all interested in your description of 
the error message. If the contents of your head were reliable, you 
wouldn't have seen the error in the first place, or would have solved 
the issue already. :-) Copy and paste your command line, and what seems 
to be the relevant part of the error.

To use pdb2gmx, you need .rtp file entries that correspond to your 
monomers. If not, you will not be able to use pdb2gmx to generate your 
topology files.


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