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

[Christian]

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? 
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