[gmx-users] Re: Re: Pyroglutamic Acid - Topology (pdb2gmx)

[Justin A. Lemkul]

Christian wrote:
> Justin Wrote:
> 
>> Did you add PGL to aminoacids.dat?  
> Yes i added PGL to this file.
>> How did you specify your termini? 
> i'm not shure where i can define this - i only found such definitions in *rtp-
> file? 

Defining termini is done with pdb2gmx -ter, but as I think about it now, that 
won't matter.

The problem comes from the special linkage between PGL and whatever the 
subsequent amino acid is - the amide is formed through the side chain.  As such, 
you will need to specify a special bond in specbond.dat before this connectivity 
will be recognized.  If this is successful, then the PHE should no longer be 
recognized as a terminal residue and thus will not receive any additional 
protonation.

The clue comes from the .rtp file.  Note that in PGL, you do not define any 
linkage to the next amino acid (using the + convention, see the other entries in 
the .rtp file), indicating that pdb2gmx will never create a linkage to any 
subsequent residue, so you have to define it.  It might be possible, for 
example, to define a bond like "CD +N" but I don't know if that will work or not.

-Justin

> the definitions there looks like this:
> [ PGL ]
>  [ atoms ]
>      N    opls_238   -0.500     1
>      H    opls_241    0.300     1
>     CA    opls_224B   0.140     1
>     HA    opls_140    0.060     1
>     CB    opls_136   -0.120     2
>    HB1    opls_140    0.060     2
>    HB2    opls_140    0.060     2
>     CG    opls_274   -0.120     3
>    HG1    opls_140    0.060     3
>    HG2    opls_140    0.060     3
>     CD    opls_235    0.500     4
>     OE    opls_236   -0.500     4
>      C    opls_235    0.500     5
>      O    opls_236   -0.500     5
>  [ bonds ]
>      N     H
>      N    CA
>     CA    HA
>     CA    CB
>     CA     C
>     CB   HB1
>     CB   HB2
>     CB    CG
>     CG   HG1
>     CG   HG2
>     CG    CD
>     CD    OE
>     CD     N
>      C     O
>     -C     N
>  [ dihedrals ] ; override some with residue-specific ones
>      N    CA    CB    CG    dih_GLU_chi1_N_C_C_C
>     CG    CB    CA     C    dih_GLU_chi1_C_C_C_CO
>  [ impropers ]
>     -C    CA     N     H    improper_Z_N_X_Y
>     CA    +N     C     O    improper_O_C_X_Y
> ;    CG   OE1    CD   OE2    improper_O_C_X_Y
> --Christian
> 
>> What's 
>> likely happening is that pdb2gmx doesn't know how to deal with PGL properly, 
>> so 
>> it's assuming PHE is the N-terminal residue and is treating it as such.
> 
>> -Justin
> 
> 
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-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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