[gmx-users] making topology file for infinite crystal

Justin A. Lemkul jalemkul at vt.edu
Sun Feb 7 17:35:28 CET 2010

Vishal Agarwal wrote:
> 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.

The "-O" is not an atom type, it indicates an oxygen atom of a previous residue. 
  It is still not clear what it is you're doing or what the actual problem is. 
If you want a resolution, you'll have to do as Mark asked and post your command 
line and the actual error message.  Remember, you're asking for free help - you 
have to make it easy for us to help you.


> Vishal
> On Sun, Feb 7, 2010 at 4:54 AM, Mark Abraham <Mark.Abraham at anu.edu.au 
> <mailto: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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> -- 
> Regards
> ***********************************************
> Vishal Agarwal
> Research Scholar
> University of Massachusetts, Amherst
> ***********************************************
> 'Your only obligation in any lifetime is to be true to yourself."
>             ---Richard Bach


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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