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

bipin singh bipinelmat at gmail.com
Wed Feb 9 07:23:47 CET 2011


Thanks for your help.....

On Wed, Feb 9, 2011 at 11:44, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:

>  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>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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-- 
*
---------------------------------
Thanks and regards
Bipin Singh
*
*
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