Re: [gmx-users] Chromophore residue patch in gromacs

2012-01-18 Thread Mark Abraham 

On 19/01/2012 3:17 PM, bharat gupta wrote:
No. I am not trying to crosslink the chromophore with nay residue but 
I have linked it with neighboring  Valine(68) and Leucine(64) by 
specifying the bonds in specbond.dat file.


You still have to go and look at residue 51 and see what is going on. 
The problem can be independent of the chromophore, as Peter was suggesting.


Mark



On Thu, Jan 19, 2012 at 12:09 PM, Peter C. Lai > wrote:


Are you crosslinking the chromophore to an atom in residue 51?

Can you generate a correct topology without the chromophore as a
check?

On 2012-01-19 11:50:37AM +0900, bharat gupta wrote:
> Hi,
>
> I have been trying to attach the chromophore of GFP in charmm ff
parameter
> files. The parameters have been obtained from a published
article. After
> making the changes as per the documentation (
>

http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field)
> , I am getting following error :-
>
> Atom CG is used in an interaction of type atom in the topology
> database, but an atom of that name was not found in residue
> number 51
>
> The chromophore residue number is 66, I don't understand why
there is an
> error for residue 51 . Please help me in rectifying this error ..
>
> Regards
>
> --
> Bharat

> --
> gmx-users mailing list gmx-users@gromacs.org

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--
==
Peter C. Lai| University of Alabama-Birmingham
Programmer/Analyst  | KAUL 752A
Genetics, Div. of Research  | 705 South 20th Street
p...@uab.edu  | Birmingham
AL 35294-4461
(205) 690-0808  |
==

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--
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com 





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Re: [gmx-users] Chromophore residue patch in gromacs

2012-01-18 Thread bharat gupta 
No. I am not trying to crosslink the chromophore with nay residue but I
have linked it with neighboring  Valine(68) and Leucine(64) by specifying
the bonds in specbond.dat file.

On Thu, Jan 19, 2012 at 12:09 PM, Peter C. Lai  wrote:

> Are you crosslinking the chromophore to an atom in residue 51?
>
> Can you generate a correct topology without the chromophore as a check?
>
> On 2012-01-19 11:50:37AM +0900, bharat gupta wrote:
> > Hi,
> >
> > I have been trying to attach the chromophore of GFP in charmm ff
> parameter
> > files. The parameters have been obtained from a published article. After
> > making the changes as per the documentation (
> >
> http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
> )
> > , I am getting following error :-
> >
> > Atom CG is used in an interaction of type atom in the topology
> > database, but an atom of that name was not found in residue
> > number 51
> >
> > The chromophore residue number is 66, I don't understand why there is an
> > error for residue 51 . Please help me in rectifying this error ..
> >
> > Regards
> >
> > --
> > Bharat
>
> > --
> > 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
>
>
> --
> ==
> Peter C. Lai| University of Alabama-Birmingham
> Programmer/Analyst  | KAUL 752A
> Genetics, Div. of Research  | 705 South 20th Street
> p...@uab.edu | Birmingham AL 35294-4461
> (205) 690-0808  |
> ==
>
> --
> 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
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>



-- 
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com
-- 
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Re: [gmx-users] Chromophore residue patch in gromacs

2012-01-18 Thread Peter C. Lai 
Are you crosslinking the chromophore to an atom in residue 51?

Can you generate a correct topology without the chromophore as a check?

On 2012-01-19 11:50:37AM +0900, bharat gupta wrote:
> Hi,
> 
> I have been trying to attach the chromophore of GFP in charmm ff parameter
> files. The parameters have been obtained from a published article. After
> making the changes as per the documentation (
> http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field)
> , I am getting following error :-
> 
> Atom CG is used in an interaction of type atom in the topology
> database, but an atom of that name was not found in residue
> number 51
> 
> The chromophore residue number is 66, I don't understand why there is an
> error for residue 51 . Please help me in rectifying this error ..
> 
> Regards
> 
> -- 
> Bharat

> -- 
> 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


-- 
==
Peter C. Lai| University of Alabama-Birmingham
Programmer/Analyst  | KAUL 752A
Genetics, Div. of Research  | 705 South 20th Street
p...@uab.edu| Birmingham AL 35294-4461
(205) 690-0808  |
==

-- 
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[gmx-users] Chromophore residue patch in gromacs

2012-01-18 Thread bharat gupta 
Hi,

I have been trying to attach the chromophore of GFP in charmm ff parameter
files. The parameters have been obtained from a published article. After
making the changes as per the documentation (
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field)
, I am getting following error :-

Atom CG is used in an interaction of type atom in the topology
database, but an atom of that name was not found in residue
number 51

The chromophore residue number is 66, I don't understand why there is an
error for residue 51 . Please help me in rectifying this error ..

Regards

-- 
Bharat
-- 
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