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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