[gmx-users] Re: No residue type for 'ARG' as a starting terminus

[Mark Abraham]

On 9/02/2011 4:56 PM, bipin singh wrote:
> Sir,
> Actually ARG is present as a ligand bound to RNA molecule....

Then you've got work to do. pdb2gmx copes well with linear polymers of 
predefined monomers, which you don't have. You will need to become very 
conversant with chapter 5 of the manual. Various how-tos on the wiki 
will help too.

One solution is to generate a topology for base-bound-to-arginine by 
hand based on the building blocks in the respective .rtp files. Check 
that topology is useful for vacuum MD of that hybrid residue. Then 
modify it to be a new .rtp entry, update the forcefield database 
accordingly. Only then can pdb2gmx deal with it.

Another is to use AMBER's leap module to generate a topology for 
base-bound-to-arginine, and convert the topology representation somehow 
(IIRC there might be a tool for that). Then proceed as above.

Mark

> On Wed, Feb 9, 2011 at 11:16, Mark Abraham <Mark.Abraham at anu.edu.au 
> <mailto:Mark.Abraham at anu.edu.au>> wrote:
>
>     On 8/02/2011 9:27 PM, bipin singh wrote:
>
>         Hi all,
>         I am getting following during while running
>         pdb2gmx for a RNA molecule....i am using amber99sb force field
>         parameters
>
>         The details of the error is as:
>
>         Fatal error:
>         In the chosen force field there is no residue type for 'ARG'
>         as a starting terminus
>         For more information and tips for troubleshooting, please
>         check the GROMACS
>         website at http://www.gromacs.org/Documentation/Errors
>
>
>     Sounds like you have an arginine residue. Why?
>
>     Mark
>     -- 
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> -- 
> /
> ---------------------------------
> Thanks and regards
> /Bipin Singh/
> /
> /
> /
>

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