[gmx-users] Unnatural amino acids- modifying topology files
David van der Spoel
spoel at xray.bmc.uu.se
Fri Aug 25 06:33:08 CEST 2006
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
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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