[gmx-users] Re: gmx-users Digest, Vol 84, Issue 177

[Gerrit Groenhof]

> 
>   4. PYP Connection (Taylor Kaplan)


Are the connections between the chromophore and cysteine there? You can check this by scanning your topology file for the indices of the sulphur and C1 atom in the [ bonds ] section. 

You can use the specbond the attach the chromophore to the protein. THis so far always worked for us.

hope it helps,

Gerrit



> Message: 4
> Date: Thu, 21 Apr 2011 00:48:07 -0700 (PDT)
> From: Taylor Kaplan <taylor_kaplan at yahoo.com>
> Subject: [gmx-users] PYP Connection
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <441414.8442.qm at web36601.mail.mud.yahoo.com>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> Hi Rama,
> 
>    I was looking at the tdb files for the amber03 force field ( I didn't change anything, i just read with the cat command ), anyways I didn't see anything written in the tdb -n or -c terminal files. After reading the gromacs manual on topology files, it said that residue connection types and such are specified through the tdb file. I'm only guessing that since the chromophore isn't an amino acid that it may have a different connection deviating from the traditional -n or -c terminals. So I was wondering if the amber force field was using the .tdb files that comes standard with gromacs ,... which I'm pretty sure lacks the type of connection that pyp makes with the protein. So to fix this problem, do we need to make or modify the .tdb file for the chromophore, or is the .tdb file of no concern? 
> 
> Thanks,
> 
> Taylor
> 
> --- On Wed, 4/20/11, Ramachandran G <gtrama at gmail.com> wrote:
> 
> From: Ramachandran G <gtrama at gmail.com>
> Subject: Re: [gmx-users] PYP chromophore force field
> To: "Peter C. Lai" <pcl at uab.edu>
> Cc: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> Date: Wednesday, April 20, 2011, 5:12 PM
> 
> 
> Yes, you are right, the chromophore(p-coumaric acid) is covalently bonded to the Sulphur(S) atom of the Cys-69 residue.
> But I specified the covalent bond in my topology.
> 
> [ bonds]
>  C   +SG
> 
> [ angles ]
> 
>       O    C   +SG   
>      CA1   C   +SG   
>       C  +SG   +CB  
> 
> [ dihedrals ]
>       O     C  +SG    +CB
>      CA1    C  +SG    +CB
>      HA2   CA1   C   +SG
>      CA2   CA1   C   +SG
>       C   +SG  +CB   +CA
> 
>       C   +SG  +CB   +HB1
>       C   +SG  +CB   +HB2
> 
> After doing pdb2gmx, i got the right structure. But the chromophore flies away after minimising. 
> 
> 
> Thanks
> Rama
> 
> On Wed, Apr 20, 2011 at 4:57 PM, Peter C. Lai <pcl at uab.edu> wrote:
> 
> Isn't the chromophore supposed to be covalently bonded to the protein?
> 
> My cursory search shows Vengris et al 2004 in Biophys. J. citing Baca et al
> 
> 1994 and van Beeumen et al 1993: "This small 125-residue protein contains a
> 
> p-coumaric acid chromophore that is covalently bound to the protein backbone
> 
> via a thiol-ester cysteine linkage Cys-69"...
> 
> 
> 
> Maybe you forgot to specify a covalent bond in your topology...
> 
> 
> 
> On 2011-04-20 06:46:54PM -0500, Ramachandran G wrote:
> 
>> Hi gromacs users,
> 
>>      I am working on Photo active yellow protein.
> 
>> 
> 
>>     Although i successfully build the force field and patched the chromophore to the protein.
> 
>> After energy minimizing the protein, the chromophore flies away separately. I don't know whether i am missing anything?
> 
>> Please help.
> 
>> Rama
> 
>> 
> 
>> 
> 
> 
> 
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> 
> 
> 
> 
> --
> 
> ===============================================================
> 
> Peter C. Lai                 | University of Alabama-Birmingham
> 
> Programmer/Analyst           | BEC 257
> 
> Genetics, Div. of Research   | 1150 10th Avenue South
> 
> pcl at uab.edu                  | Birmingham AL 35294-4461
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