[gmx-users] making topology file for infinite crystal

[Vishal Agarwal]

Dear Justin,

I am trying to make topology file for cellulose II. The monomer unit is
glucose (residue type GLCA). I do the following:

pdb2gmx -f cellulose.gro


I am getting the following error while using pdbgmx.

"Fatal Error:
Atom -O not found in residue 2 while adding improper"

Atom type "O" is actually not part of the GLCA residue. Only atom type OA is
part of GLCA residue.
Do I need to modify the rtp entry to suit my system or does this error
corresponds to something else ?

Your help is appreciated.
Thanks,
Vishal

On Sun, Feb 7, 2010 at 11:35 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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.
>
> -Justin
>
>  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
>>    --    gmx-users mailing list    gmx-users at gromacs.org
>>    <mailto:gmx-users at gromacs.org>
>>
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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
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
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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
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