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

2011-02-08 Thread bipin singh 
Thanks for your help.

On Wed, Feb 9, 2011 at 11:44, Mark Abraham  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 wrote:
>
>> On 8/02/2011 9:27 PM, bipin singh wrote:
>>
>>> Hi all,
>>> I am getting following during while running
>>> pdb2gmx for a RNA moleculei 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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-- 
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Thanks and regards
Bipin Singh
*
*
*
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Re: [gmx-users] Re: No residue type for 'ARG' as a starting terminus

2011-02-08 Thread 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 > wrote:


On 8/02/2011 9:27 PM, bipin singh wrote:

Hi all,
I am getting following during while running
pdb2gmx for a RNA moleculei 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@gromacs.org


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--
/
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Thanks and regards
/Bipin Singh/
/
/
/



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

2011-02-08 Thread bipin singh 
Sir,
Actually ARG is present as a ligand bound to RNA molecule


On Wed, Feb 9, 2011 at 11:16, Mark Abraham  wrote:

> On 8/02/2011 9:27 PM, bipin singh wrote:
>
>> Hi all,
>> I am getting following during while running
>> pdb2gmx for a RNA moleculei 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 listgmx-users@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-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
*
-
Thanks and regards
Bipin Singh
*
*
*
-- 
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Re: [gmx-users] Re: No residue type for 'ARG' as a starting terminus

2011-02-08 Thread Mark Abraham 

On 8/02/2011 9:27 PM, bipin singh wrote:

Hi all,
I am getting following during while running
pdb2gmx for a RNA moleculei 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 listgmx-users@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!
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[gmx-users] Re: No residue type for 'ARG' as a starting terminus

2011-02-08 Thread bipin singh 
Hi all,
I am getting following during while running
pdb2gmx for a RNA moleculei 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





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