Hello GROMACS people,
I'm trying to model a protein containing the unnatural amino acid
para-fluorophenylalanine (FPhe). I modified the aminoacid.dat file,
as well as the .hdb and .rtp files by adapting the existing entry for
PHE.
I have been able to use 'grompp' and perform a minimization of an
FPhe-containing protein. However when I perform 'grompp' I get a
warning:
>WARNING 1
[file "1U70_F.itp", line 27460]:
>No default
Proper Dih. types, using zeroes
The line in the .itp file corresponds to atoms which include the CE1,
CE2, CZ and F atoms of FPhe. I'm surprised that GROMACS is giving me a
warning because the FPh entry in the .rtp file nearly identical to that
for the PHE- the HZ atom is simply replaced by an F atom (the FPhe
entry in the .rtp file is included at the end of this message). How can I
rectify this situation?
Thanks,
Vanessa
________________________________________________________________
[ FPh ]
[ atoms ]
N amber99_34
-0.41570 1
H amber99_17
0.27190 2
CA amber99_11 -0.00240
3
HA amber99_19
0.09780 4
CB amber99_11 -0.03430
5
HB1 amber99_18
0.02950 6
HB2 amber99_18
0.02950 7
CG amber99_3
0.01180 8
CD1 amber99_3
-0.12560 9
HD1 amber99_22 0.13300
10
CE1 amber99_3 -0.17040
11
HE1 amber99_22 0.14300
12
CZ amber99_3 -0.10720
13
F amber99_16 -0.21700 14
CE2 amber99_3 -0.17040
15
HE2 amber99_22 0.14300
16
CD2 amber99_3 -0.12560
17
HD2 amber99_22 0.13300
18
C amber99_2 0.59730
19
O amber99_41 -0.56790 20
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB
HB1
CB
HB2
CB CG
CG CD1
CG CD2
CD1
HD1
CD1
CE1
CE1
HE1
CE1 CZ
CZ F
CZ CE2
CE2
HE2
CE2
CD2
CD2
HD2
C O
-C N
[ dihedrals
]
CA C +N
+H backbone_prop_1
O C +N
+H backbone_prop_2
-C N CA
CB backbone_prop_3
-C N CA
C backbone_prop_4
CA C +N
+CA backbone_prop_1
O C +N
+CA backbone_prop_1
CB CG CD1 HD1
aromatic_prop_1
CB CG CD2 HD2
aromatic_prop_1
CB CG CD1 CE1
aromatic_prop_1
CB CG CD2 CE2
aromatic_prop_1
CG
CD1 CE1 HE1
aromatic_prop_1
CG
CD2 CE2 HE2
aromatic_prop_1
CG
CD1 CE1 CZ
aromatic_prop_1
CG
CD2 CE2 CZ
aromatic_prop_1
CD1
CE1 CZ F
aromatic_prop_1
CD1 CE1 CZ CE2
aromatic_prop_1
CD2 CE2 CZ
F aromatic_prop_1
CD2 CE2 CZ CE1
aromatic_prop_1
CE1 CZ CE2 HE2
aromatic_prop_1
CE2 CZ CE1 HE1
aromatic_prop_1
HD1 CD1 CE1 HE1
aromatic_prop_1
HD2
CD2 CE2 HE2
aromatic_prop_1
HE1
CE1 CZ F
aromatic_prop_1
HE2
CE2 CZ F
aromatic_prop_1
HD1
CD1 CE1 CZ
aromatic_prop_1
HD2
CD2 CE2 CZ
aromatic_prop_1
HD1
CD1 CG CD2
aromatic_prop_1
CD1
CG CD2 HD2 aromatic_prop_1
CE1
CD1 CG CD2
aromatic_prop_1
CD1 CG CD2 CE2
aromatic_prop_1
[ impropers
]
-C CA N
H
CA +N C
O
CG
CE2 CD2 HD2
CZ
CD2 CE2 HE2
CE1
CE2 CZ F
CD1 CZ CE1 HE1
CG
CE1 CD1 HD1
CD1
CD2 CG CB
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