Vanessa Oklejas wrote:
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
this may be slightly confusing, but OPLS uses the cosine based proper
dihedrals (in GROMOS speak) to implement *improper* dihedrals, i.e. to
prevent your F from going out of the plane. You therefore have to
specify parameters in the improper section below.
/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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--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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