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

[bipin singh]

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
>>  --
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>
>
>
> --
> *
> ---------------------------------
> Thanks and regards
>  Bipin Singh
> *
> *
> *
>
>
>
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
*
---------------------------------
Thanks and regards
Bipin Singh
*
*
*
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110209/f85b68de/attachment.html>