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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--
========================================

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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