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
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