[gmx-users] making topology file for infinite crystal

Vishal Agarwal vishal.iitian at gmail.com
Sun Feb 7 17:29:58 CET 2010

Dear Mark,

What I meant over here is the missing oxygen  (-O) which pdbgmx complains
about is not a part of .rtp entry. There is no such type of oxygen specified
in any of the .atp entry of the forcefield I am using.


On Sun, Feb 7, 2010 at 4:54 AM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

> 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.
> Mark
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Vishal Agarwal
Research Scholar
University of Massachusetts, Amherst
'Your only obligation in any lifetime is to be true to yourself."
            ---Richard Bach
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