Re: AMBER: modifications to force field for Fe4S4 cubane from Ilyas Yildirim on 2007-11-27 (Amber Archive Nov 2007)

From: Ilyas Yildirim <yildirim.pas.rochester.edu>
Date: Tue, 27 Nov 2007 14:29:58 -0500 (EST)

I am not a protein person; so let me see if I understood your system. You
have a residue which is called FES. You want this FES residue to bind to 4
CYS residues. And these 4 CYS residues are in different places in the
protein. And for these bonds, you have parameters given in frcmod file,
right?

A similar question was asked before in the amber mailing list. I do not
think that you can have 1 FES and 4 CYS residues where CYS residues are
connected to 4 different atoms of FES residue. One solution I can think of
is first to create the inpcrd/prmtop files without having these bindings
to CYS residues and then to put some distance restraints to those bonds in
the MD simulations. Other than this solution, I do not think that you can
connect the FES residue to 4 CYS residues (another solution is to create 1
residue which includes the FES and 4 CYS residues, but this will not work
either because I do not think that you can specify in .lib file 4 terminal
points - only 2 terminals can be specified). Hope this helps. Good luck.

Best regards,

On Tue, 27 Nov 2007, Boutheïna Kerkeni wrote:

> Ok Thanks very much for pointing this to me.
> Do you please have any idea how to create topology and coordinate
> file for the CYF+FES residues?
> because fes.pdb is cut out from cyf.pdb (but the latter has modified
> cysteines now and also there is a problem of shared residue number!)
> from fes.pdb and cyf.pdb, fes.frcmod, and cyf.frcmod
> Thanks very much for your help with this!!
> Here are my fes.pdb and cyf.pdb
> HETATM 1985 S1 FES S 267 34.447 34.094 111.212 1.00
> 2.00 S
> HETATM 1986 S2 FES S 267 33.848 33.897 114.767 1.00
> 2.00 S
> HETATM 1987 S3 FES S 267 36.832 35.519 113.511 1.00
> 2.00 S
> HETATM 1988 S4 FES S 267 36.543 31.924 113.185 1.00
> 2.00 S
>
> HETATM 1981 FE1 FES S 17 34.634 35.304 113.224 1.00
> 2.00 FE
> ATOM 113 CB FES S 17 31.984 37.285 113.115 1.00
> 2.00 C
> ATOM 114 SG FES S 17 33.787 37.364 113.280 1.00
> 2.00 S
>
> HETATM 1982 FE2 FES S 112 34.363 32.588 112.931 1.00
> 2.00 FE
> ATOM 809 CB FES S 112 33.352 29.697 112.009 1.00
> 2.00 C
> ATOM 810 SG FES S 112 33.038 30.838 113.289 1.00
> 2.00 S
>
> HETATM 1983 FE3 FES S 148 36.083 33.652 114.690 1.00
> 2.76 FE
> ATOM 1049 CB FES S 148 38.546 32.478 116.891 1.00
> 2.00 C
> ATOM 1050 SG FES S 148 36.839 33.007 116.844 1.00
> 2.00 S
>
> HETATM 1984 FE4 FES S 20 36.595 33.848 111.968 1.00
> 2.00 FE
> ATOM 130 CB FES S 20 37.983 34.648 108.903 1.00
> 2.00 C
> ATOM 131 SG FES S 20 38.200 33.520 110.342 1.00
> 2.00 S
>
> cyf.pdb:
>
> ATOM 109 N CYF S 17 31.447 36.047 111.043 1.00
> 2.00 N
> ATOM 110 CA CYF S 17 31.456 37.369 111.671 1.00
> 2.00 C
> ATOM 111 C CYF S 17 32.269 38.354 110.833 1.00
> 2.00 C
> ATOM 112 O CYF S 17 32.279 39.559 111.015 1.00
> 2.00 O
>
> ATOM 805 N CYF S 112 35.516 28.670 112.650 1.00
> 2.00 N
> ATOM 806 CA CYF S 112 34.115 28.402 112.230 1.00
> 2.00 C
> ATOM 807 C CYF S 112 34.090 27.532 110.970 1.00
> 2.00 C
> ATOM 808 O CYF S 112 33.271 26.611 110.929 1.00
> 2.00 O
>
> ATOM 1045 N CYF S 148 40.614 32.189 115.664 1.00
> 2.63 N
> ATOM 1046 CA CYF S 148 39.394 32.998 115.724 1.00
> 2.00 C
> ATOM 1047 C CYF S 148 39.670 34.466 115.933 1.00
> 3.11 C
> ATOM 1048 O CYF S 148 39.313 34.967 117.017 1.00
> 3.02 O
>
> ATOM 126 N CYF S 20 37.429 36.929 109.880 1.00
> 2.00 N
> ATOM 127 CA CYF S 20 38.407 36.075 109.145 1.00
> 2.00 C
> ATOM 128 C CYF S 20 38.867 36.881 107.926 1.00
> 2.00 C
> ATOM 129 O CYF S 20 40.092 36.948 107.685 1.00
> 2.00 O
>
> On 27 Nov 2007, at 15:02, Ilyas Yildirim wrote:
>
> > The format of your frcmod file is not fully right and also there
> > are some
> > missing parameters in it. Use the following format, but fill in
> > the ???
> > parts. The missing parts are the atomic polarizabilities, which have
> > different values for different types. Check out the .parm files in
> >
> > $AMBERHOME/dat/leap/parm
> >
> > to decide which value can be used for this parameter in your system.
> >
> > ---------- .frcmod ----------------------
> > ## modifications to force field for CYF special cysteine
> >
> > MASS
> > N 14.01 0.530
> > C 12.01 ???
> > O 16.00 ???
> >
> > BOND
> > N -CA 481.0 1.34
> >
> > ANGLE
> > N -CA-C 70. 120.1
> > CA-C -O 70. 120.
> >
> > DIHE
> >
> > NONB
> > ----------------------------------------
> > For more information about the format of frcmod file, check out the
> > following website;
> >
> > http://amber.scripps.edu/formats.html#frcmod
> >
> > Best regards,
> >
> > On Tue, 27 Nov 2007, Boutheïna Kerkeni wrote:
> >
> >>
> >>
> >>
> >>>
> >>> Dear Amber users
> >>>
> >>> anyone could help with my inquiry?
> >>> Thanks in advance
> >>> Regards
> >>> Boutheina
> >>>
> >>> i cut out from the whole pdb a file for the Fe4S4C4 residue FES
> >>> and a file for the 4 cysteines CA-N-C-O residue CYF.
> >>>
> >>> After determining .frcmod charges etc for FES, I need to bond it to
> >>> the 4 above
> >>> cysteines. I had a problem with this/
> >>>
> >>> Cys file new residue CYF
> >>> ATOM 109 N CYF S 17 31.447 36.047 111.043 1.00 =20
> >>> 2.00 N
> >>> ATOM 110 CA CYF S 17 31.456 37.369 111.671 1.00 =20
> >>> 2.00 C
> >>> ATOM 111 C CYF S 17 32.269 38.354 110.833 1.00 =20
> >>> 2.00 C
> >>> ATOM 112 O CYF S 17 32.279 39.559 111.015 1.00 =20
> >>> 2.00 O
> >>>
> >>> ATOM 805 N CYF S 112 35.516 28.670 112.650 1.00 =20
> >>> 2.00 N
> >>> ATOM 806 CA CYF S 112 34.115 28.402 112.230 1.00 =20
> >>> 2.00 C
> >>> ATOM 807 C CYF S 112 34.090 27.532 110.970 1.00 =20
> >>> 2.00 C
> >>> ATOM 808 O CYF S 112 33.271 26.611 110.929 1.00 =20
> >>> 2.00 O
> >>>
> >>> ATOM 1045 N CYF S 148 40.614 32.189 115.664 1.00 =20
> >>> 2.63 N
> >>> ATOM 1046 CA CYF S 148 39.394 32.998 115.724 1.00 =20
> >>> 2.00 C
> >>> ATOM 1047 C CYF S 148 39.670 34.466 115.933 1.00 =20
> >>> 3.11 C
> >>> ATOM 1048 O CYF S 148 39.313 34.967 117.017 1.00 =20
> >>> 3.02 O
> >>>
> >>> ATOM 126 N CYF S 20 37.429 36.929 109.880 1.00 =20
> >>> 2.00 N
> >>> ATOM 127 CA CYF S 20 38.407 36.075 109.145 1.00 =20
> >>> 2.00 C
> >>> ATOM 128 C CYF S 20 38.867 36.881 107.926 1.00 =20
> >>> 2.00 C
> >>> ATOM 129 O CYF S 20 40.092 36.948 107.685 1.00 =20
> >>> 2.00 O
> >>>
> >>> Xleap creates the bonds as I want, but when I try to create top and
> >>> coord files/
> >>>> saveamberparm x2 x2.prmtop x2.inpcrd
> >>>
> >>> xleap complains about missing bond and angle param/
> >>> N-CA
> >>> N-CA-C
> >>> CA-C-O
> >>>
> >>> should I create a cyf.frcmod fromm amber library? is CM=3DC? O=3DOH?
> >>> # modifications to force field for CYF special cysteine
> >>>
> >>> MASS
> >>> N 14.00674
> >>> C 12.0107
> >>> O 15.9994
> >>>
> >>> BOND
> >>> N CA 481.0 1.34
> >>>
> >>> ANGLE
> >>> N CA C 70. 120.1
> >>> CA C O 70. 120.
> >>>
> >>> DIHE
> >>>
> >>> NONB
> >>>
> >>> I have actually tried to do this, and created x2.prmtop and
> >>> x2.inpcrd =20=
> >>>
> >>> but the newly formed x2.inpcrd.pdb
> >>> does not contain the cubane!! here it is:
> >>> REMARK
> >>> ATOM 1 N CYF 1 31.447 36.047 111.043
> >>> ATOM 2 CA CYF 1 31.456 37.369 111.671
> >>> ATOM 3 C CYF 1 32.269 38.354 110.833
> >>> ATOM 4 O CYF 1 32.279 39.559 111.015
> >>> TER
> >>> ATOM 5 N CYF 2 35.516 28.670 112.650
> >>> ATOM 6 CA CYF 2 34.115 28.402 112.230
> >>> ATOM 7 C CYF 2 34.090 27.532 110.970
> >>> ATOM 8 O CYF 2 33.271 26.611 110.929
> >>> TER
> >>> ATOM 9 N CYF 3 40.614 32.189 115.664
> >>> ATOM 10 CA CYF 3 39.394 32.998 115.724
> >>> ATOM 11 C CYF 3 39.670 34.466 115.933
> >>> ATOM 12 O CYF 3 39.313 34.967 117.017
> >>> TER
> >>> ATOM 13 N CYF 4 37.429 36.929 109.880
> >>> ATOM 14 CA CYF 4 38.407 36.075 109.145
> >>> ATOM 15 C CYF 4 38.867 36.881 107.926
> >>> ATOM 16 O CYF 4 40.092 36.948 107.685
> >>> TER
> >>> END
> >>>
> >>>
> >>> Any help is very much appreciated.
> >>> Regards
> >>> Begin forwarded message:
> >>>
> >>>> From: Bouthe=EFna Kerkeni <b.kerkeni.ucl.ac.uk>
> >>>> Date: 23 November 2007 19:24:43 GMT
> >>>> To: David A. Case <case.scripps.edu>
> >>>> Subject: Re: AMBER: modifications to force field for Fe4S4 cubane
> >>>>
> >>>> I have tryied to use the bond command but xleap complained: =20
> >>>> (details are below:)
> >>>>
> >>>>> bond x1.268.CB x2.268.CA
> >>>> bond: Argument #2 is type String must be of type: [atom]
> >>>> usage: bond <atom1> <atom2> [order]
> >>>>> bond x1.269.CB x2.269.CA
> >>>> bond: Argument #2 is type String must be of type: [atom]
> >>>> usage: bond <atom1> <atom2> [order]
> >>>>> bond x1.270.CB x2.270.CA
> >>>> bond: Argument #2 is type String must be of type: [atom]
> >>>> usage: bond <atom1> <atom2> [order]
> >>>>> bond x1.271.CB x2.271.CA
> >>>> bond: Argument #2 is type String must be of type: [atom]
> >>>> usage: bond <atom1> <atom2> [order]
> >>>>
> >>>> This is my fes.pdb
> >>>> HETATM 1985 S1 FES S 267 34.447 34.094 111.212 1.00 =20
> >>>> 2.00 S
> >>>> HETATM 1986 S2 FES S 267 33.848 33.897 114.767 1.00 =20
> >>>> 2.00 S
> >>>> HETATM 1987 S3 FES S 267 36.832 35.519 113.511 1.00 =20
> >>>> 2.00 S
> >>>> HETATM 1988 S4 FES S 267 36.543 31.924 113.185 1.00 =20
> >>>> 2.00 S
> >>>>
> >>>> HETATM 1981 FE1 FES S 17 34.634 35.304 113.224 1.00 =20
> >>>> 2.00 FE
> >>>> ATOM 113 CB FES S 17 31.984 37.285 113.115 1.00 =20
> >>>> 2.00 C
> >>>> ATOM 114 SG FES S 17 33.787 37.364 113.280 1.00 =20
> >>>> 2.00 S
> >>>>
> >>>> HETATM 1982 FE2 FES S 112 34.363 32.588 112.931 1.00 =20
> >>>> 2.00 FE
> >>>> ATOM 809 CB FES S 112 33.352 29.697 112.009 1.00 =20
> >>>> 2.00 C
> >>>> ATOM 810 SG FES S 112 33.038 30.838 113.289 1.00 =20
> >>>> 2.00 S
> >>>>
> >>>> HETATM 1983 FE3 FES S 148 36.083 33.652 114.690 1.00 =20
> >>>> 2.76 FE
> >>>> ATOM 1049 CB FES S 148 38.546 32.478 116.891 1.00 =20
> >>>> 2.00 C
> >>>> ATOM 1050 SG FES S 148 36.839 33.007 116.844 1.00 =20
> >>>> 2.00 S
> >>>>
> >>>> HETATM 1984 FE4 FES S 20 36.595 33.848 111.968 1.00 =20
> >>>> 2.00 FE
> >>>> ATOM 130 CB FES S 20 37.983 34.648 108.903 1.00 =20
> >>>> 2.00 C
> >>>> ATOM 131 SG FES S 20 38.200 33.520 110.342 1.00 =20
> >>>> 2.00 S
> >>>>
> >>>> to which I created FES.lib (after adding charges, and loading =20
> >>>> the .frcmod file to xleap)
> >>>>
> >>>> This is my modified(creation of 4 CYF residues) initial pdb file
> >>>> =20
> >>>> (cut out from the enzyme)
> >>>> file.pdb
> >>>> HETATM 1985 S1 FES S 267 34.447 34.094 111.212 1.00 =20
> >>>> 2.00 S
> >>>> HETATM 1986 S2 FES S 267 33.848 33.897 114.767 1.00 =20
> >>>> 2.00 S
> >>>> HETATM 1987 S3 FES S 267 36.832 35.519 113.511 1.00 =20
> >>>> 2.00 S
> >>>> HETATM 1988 S4 FES S 267 36.543 31.924 113.185 1.00 =20
> >>>> 2.00 S
> >>>>
> >>>> HETATM 1981 FE1 FES S 17 34.634 35.304 113.224 1.00 =20
> >>>> 2.00 FE
> >>>> ATOM 113 CB FES S 17 31.984 37.285 113.115 1.00 =20
> >>>> 2.00 C
> >>>> ATOM 114 SG FES S 17 33.787 37.364 113.280 1.00 =20
> >>>> 2.00 S
> >>>> ATOM 109 N CYF S 17 31.447 36.047 111.043 1.00 =20
> >>>> 2.00 N
> >>>> ATOM 110 CA CYF S 17 31.456 37.369 111.671 1.00 =20
> >>>> 2.00 C
> >>>> ATOM 111 C CYF S 17 32.269 38.354 110.833 1.00 =20
> >>>> 2.00 C
> >>>> ATOM 112 O CYF S 17 32.279 39.559 111.015 1.00 =20
> >>>> 2.00 O
> >>>>
> >>>> HETATM 1982 FE2 FES S 112 34.363 32.588 112.931 1.00 =20
> >>>> 2.00 FE
> >>>> ATOM 809 CB FES S 112 33.352 29.697 112.009 1.00 =20
> >>>> 2.00 C
> >>>> ATOM 810 SG FES S 112 33.038 30.838 113.289 1.00 =20
> >>>> 2.00 S
> >>>> ATOM 805 N CYF S 112 35.516 28.670 112.650 1.00 =20
> >>>> 2.00 N
> >>>> ATOM 806 CA CYF S 112 34.115 28.402 112.230 1.00 =20
> >>>> 2.00 C
> >>>> ATOM 807 C CYF S 112 34.090 27.532 110.970 1.00 =20
> >>>> 2.00 C
> >>>> ATOM 808 O CYF S 112 33.271 26.611 110.929 1.00 =20
> >>>> 2.00 O
> >>>>
> >>>> HETATM 1983 FE3 FES S 148 36.083 33.652 114.690 1.00 =20
> >>>> 2.76 FE
> >>>> ATOM 1049 CB FES S 148 38.546 32.478 116.891 1.00 =20
> >>>> 2.00 C
> >>>> ATOM 1050 SG FES S 148 36.839 33.007 116.844 1.00 =20
> >>>> 2.00 S
> >>>> ATOM 1045 N CYF S 148 40.614 32.189 115.664 1.00 =20
> >>>> 2.63 N
> >>>> ATOM 1046 CA CYF S 148 39.394 32.998 115.724 1.00 =20
> >>>> 2.00 C
> >>>> ATOM 1047 C CYF S 148 39.670 34.466 115.933 1.00 =20
> >>>> 3.11 C
> >>>> ATOM 1048 O CYF S 148 39.313 34.967 117.017 1.00 =20
> >>>> 3.02 O
> >>>>
> >>>> HETATM 1984 FE4 FES S 20 36.595 33.848 111.968 1.00 =20
> >>>> 2.00 FE
> >>>> ATOM 130 CB FES S 20 37.983 34.648 108.903 1.00 =20
> >>>> 2.00 C
> >>>> ATOM 131 SG FES S 20 38.200 33.520 110.342 1.00 =20
> >>>> 2.00 S
> >>>> ATOM 126 N CYF S 20 37.429 36.929 109.880 1.00 =20
> >>>> 2.00 N
> >>>> ATOM 127 CA CYF S 20 38.407 36.075 109.145 1.00 =20
> >>>> 2.00 C
> >>>> ATOM 128 C CYF S 20 38.867 36.881 107.926 1.00 =20
> >>>> 2.00 C
> >>>> ATOM 129 O CYF S 20 40.092 36.948 107.685 1.00 =20
> >>>> 2.00 O
> >>>>
> >>>> In xleap I did:
> >>>>> loadoff FES.lib
> >>>>> x1=3Dloadpdb fes.pdb
> >>>> Loading PDB file: ./fes.pdb
> >>>> Enter zPdbReadScan from call depth 0.
> >>>> Exit zPdbReadScan from call depth 0.
> >>>> Matching PDB residue names to LEaP variables.
> >>>> (Residue 0: FES, Terminal/beginning, was not found in name map.)
> >>>> (Residue 1: FES, Nonterminal, was not found in name map.)
> >>>> (Residue 2: FES, Nonterminal, was not found in name map.)
> >>>> (Residue 3: FES, Nonterminal, was not found in name map.)
> >>>> (Residue 4: FES, Terminal/last, was not found in name map.)
> >>>> Added missing heavy atom: .R<FES 269>.A<FE2 1>
> >>>> Added missing heavy atom: .R<FES 269>.A<SG 3>
> >>>> Added missing heavy atom: .R<FES 269>.A<CB 2>
> >>>> Added missing heavy atom: .R<FES 271>.A<FE4 1>
> >>>> Added missing heavy atom: .R<FES 271>.A<SG 3>
> >>>> Added missing heavy atom: .R<FES 271>.A<CB 2>
> >>>> Added missing heavy atom: .R<FES 270>.A<FE3 1>
> >>>> Added missing heavy atom: .R<FES 270>.A<SG 3>
> >>>> Added missing heavy atom: .R<FES 270>.A<CB 2>
> >>>> Added missing heavy atom: .R<FES 268>.A<FE1 1>
> >>>> Added missing heavy atom: .R<FES 268>.A<SG 3>
> >>>> Added missing heavy atom: .R<FES 268>.A<CB 2>
> >>>> Starting new chain with
> >>>> Created a new atom named: FE1 within residue: .R<FES 268>
> >>>> Created a new atom named: CB within residue: .R<FES 268>
> >>>> Created a new atom named: SG within residue: .R<FES 268>
> >>>> Added missing heavy atom: .R<FES 268>.A<S4 4>
> >>>> Added missing heavy atom: .R<FES 270>.A<FE2 1>
> >>>> Added missing heavy atom: .R<FES 272>.A<FE4 1>
> >>>> Added missing heavy atom: .R<FES 271>.A<FE3 1>
> >>>> Added missing heavy atom: .R<FES 268>.A<S1 1>
> >>>> Added missing heavy atom: .R<FES 268>.A<S2 2>
> >>>> Added missing heavy atom: .R<FES 270>.A<SG 3>
> >>>> Added missing heavy atom: .R<FES 268>.A<S3 3>
> >>>> Added missing heavy atom: .R<FES 272>.A<SG 3>
> >>>> Added missing heavy atom: .R<FES 271>.A<SG 3>
> >>>> Added missing heavy atom: .R<FES 269>.A<FE1 1>
> >>>> Added missing heavy atom: .R<FES 270>.A<CB 2>
> >>>> Added missing heavy atom: .R<FES 272>.A<CB 2>
> >>>> Added missing heavy atom: .R<FES 271>.A<CB 2>
> >>>> Added missing heavy atom: .R<FES 269>.A<SG 3>
> >>>> Added missing heavy atom: .R<FES 269>.A<CB 2>
> >>>> Starting new chain with
> >>>> Created a new atom named: FE2 within residue: .R<FES 269>
> >>>> Created a new atom named: CB within residue: .R<FES 269>
> >>>> Created a new atom named: SG within residue: .R<FES 269>
> >>>> Added missing heavy atom: .R<FES 269>.A<S4 4>
> >>>> Added missing heavy atom: .R<FES 271>.A<FE2 1>
> >>>> Added missing heavy atom: .R<FES 273>.A<FE4 1>
> >>>> Added missing heavy atom: .R<FES 272>.A<FE3 1>
> >>>> Added missing heavy atom: .R<FES 269>.A<S1 1>
> >>>> Added missing heavy atom: .R<FES 269>.A<S2 2>
> >>>> Added missing heavy atom: .R<FES 271>.A<SG 3>
> >>>> Added missing heavy atom: .R<FES 269>.A<S3 3>
> >>>> Added missing heavy atom: .R<FES 273>.A<SG 3>
> >>>> Added missing heavy atom: .R<FES 272>.A<SG 3>
> >>>> Added missing heavy atom: .R<FES 270>.A<FE1 1>
> >>>> Added missing heavy atom: .R<FES 271>.A<CB 2>
> >>>> Added missing heavy atom: .R<FES 273>.A<CB 2>
> >>>> Added missing heavy atom: .R<FES 272>.A<CB 2>
> >>>> Added missing heavy atom: .R<FES 270>.A<SG 3>
> >>>> Added missing heavy atom: .R<FES 270>.A<CB 2>
> >>>> Starting new chain with
> >>>> Created a new atom named: FE3 within residue: .R<FES 270>
> >>>> Created a new atom named: CB within residue: .R<FES 270>
> >>>> Created a new atom named: SG within residue: .R<FES 270>
> >>>> Added missing heavy atom: .R<FES 270>.A<S4 4>
> >>>> Added missing heavy atom: .R<FES 272>.A<FE2 1>
> >>>> Added missing heavy atom: .R<FES 274>.A<FE4 1>
> >>>> Added missing heavy atom: .R<FES 273>.A<FE3 1>
> >>>> Added missing heavy atom: .R<FES 270>.A<S1 1>
> >>>> Added missing heavy atom: .R<FES 270>.A<S2 2>
> >>>> Added missing heavy atom: .R<FES 272>.A<SG 3>
> >>>> Added missing heavy atom: .R<FES 270>.A<S3 3>
> >>>> Added missing heavy atom: .R<FES 274>.A<SG 3>
> >>>> Added missing heavy atom: .R<FES 273>.A<SG 3>
> >>>> Added missing heavy atom: .R<FES 271>.A<FE1 1>
> >>>> Added missing heavy atom: .R<FES 272>.A<CB 2>
> >>>> Added missing heavy atom: .R<FES 274>.A<CB 2>
> >>>> Added missing heavy atom: .R<FES 273>.A<CB 2>
> >>>> Added missing heavy atom: .R<FES 271>.A<SG 3>
> >>>> Added missing heavy atom: .R<FES 271>.A<CB 2>
> >>>> Starting new chain with
> >>>> Created a new atom named: FE4 within residue: .R<FES 271>
> >>>> Created a new atom named: CB within residue: .R<FES 271>
> >>>> Created a new atom named: SG within residue: .R<FES 271>
> >>>> Added missing heavy atom: .R<FES 271>.A<S4 4>
> >>>> Added missing heavy atom: .R<FES 273>.A<FE2 1>
> >>>> Added missing heavy atom: .R<FES 275>.A<FE4 1>
> >>>> Added missing heavy atom: .R<FES 274>.A<FE3 1>
> >>>> Added missing heavy atom: .R<FES 271>.A<S1 1>
> >>>> Added missing heavy atom: .R<FES 271>.A<S2 2>
> >>>> Added missing heavy atom: .R<FES 273>.A<SG 3>
> >>>> Added missing heavy atom: .R<FES 271>.A<S3 3>
> >>>> Added missing heavy atom: .R<FES 275>.A<SG 3>
> >>>> Added missing heavy atom: .R<FES 274>.A<SG 3>
> >>>> Added missing heavy atom: .R<FES 272>.A<FE1 1>
> >>>> Added missing heavy atom: .R<FES 273>.A<CB 2>
> >>>> Added missing heavy atom: .R<FES 275>.A<CB 2>
> >>>> Added missing heavy atom: .R<FES 274>.A<CB 2>
> >>>> Added missing heavy atom: .R<FES 272>.A<SG 3>
> >>>> Added missing heavy atom: .R<FES 272>.A<CB 2>
> >>>> total atoms in file: 16
> >>>> Leap added 76 missing atoms according to residue templates:
> >>>> 76 Heavy
> >>>> The file contained 12 atoms not in residue templates
> >>>>
> >>>>> x2=3Dloadpdb original.pdb
> >>>>> x2=3Dloadpdb original.pdb
> >>>> Loading PDB file: ./original.pdb
> >>>> Enter zPdbReadScan from call depth 0.
> >>>> Warning: name change in pdb file residue 17 ;
> >>>> this residue is split into FES and CYF.
> >>>> Warning: name change in pdb file residue 112 ;
> >>>> this residue is split into FES and CYF.
> >>>> Warning: name change in pdb file residue 148 ;
> >>>> this residue is split into FES and CYF.
> >>>> Warning: name change in pdb file residue 20 ;
> >>>> this residue is split into FES and CYF.
> >>>> 4 residues had naming warnings.
> >>>> There are split residues;
> >>>> residue sequence numbers will not correspond to those in the pdb.
> >>>> Exit zPdbReadScan from call depth 0.
> >>>> Matching PDB residue names to LEaP variables.
> >>>> (Residue 0: FES, Terminal/beginning, was not found in name map.)
> >>>> (Residue 1: FES, Nonterminal, was not found in name map.)
> >>>> (Residue 2: CYF, Nonterminal, was not found in name map.)
> >>>> Unknown residue: CYF number: 2 type: Nonterminal
> >>>> (Residue 3: FES, Nonterminal, was not found in name map.)
> >>>> (Residue 4: CYF, Nonterminal, was not found in name map.)
> >>>> Unknown residue: CYF number: 4 type: Nonterminal
> >>>> (Residue 5: FES, Nonterminal, was not found in name map.)
> >>>> (Residue 6: CYF, Nonterminal, was not found in name map.)
> >>>> Unknown residue: CYF number: 6 type: Nonterminal
> >>>> (Residue 7: FES, Nonterminal, was not found in name map.)
> >>>> (Residue 8: CYF, Terminal/last, was not found in name map.)
> >>>> Unknown residue: CYF number: 8 type: Terminal/last
> >>>> ..relaxing end constraints to try for a dbase match
> >>>> -no luck
> >>>> Added missing heavy atom: .R<FES 269>.A<FE2 1>
> >>>> Added missing heavy atom: .R<FES 269>.A<SG 3>
> >>>> Added missing heavy atom: .R<FES 269>.A<CB 2>
> >>>> Added missing heavy atom: .R<FES 271>.A<FE4 1>
> >>>> Added missing heavy atom: .R<FES 271>.A<SG 3>
> >>>> Added missing heavy atom: .R<FES 271>.A<CB 2>
> >>>> Added missing heavy atom: .R<FES 270>.A<FE3 1>
> >>>> Added missing heavy atom: .R<FES 270>.A<SG 3>
> >>>> Added missing heavy atom: .R<FES 270>.A<CB 2>
> >>>> Added missing heavy atom: .R<FES 268>.A<FE1 1>
> >>>> Added missing heavy atom: .R<FES 268>.A<SG 3>
> >>>> Added missing heavy atom: .R<FES 268>.A<CB 2>
> >>>> Starting new chain with
> >>>> Created a new atom named: FE1 within residue: .R<FES 268>
> >>>> Created a new atom named: CB within residue: .R<FES 268>
> >>>> Created a new atom named: SG within residue: .R<FES 268>
> >>>> Added missing heavy atom: .R<FES 268>.A<S4 4>
> >>>> Added missing heavy atom: .R<FES 270>.A<FE2 1>
> >>>> Added missing heavy atom: .R<FES 272>.A<FE4 1>
> >>>> Added missing heavy atom: .R<FES 271>.A<FE3 1>
> >>>> Added missing heavy atom: .R<FES 268>.A<S1 1>
> >>>> Added missing heavy atom: .R<FES 268>.A<S2 2>
> >>>> Added missing heavy atom: .R<FES 270>.A<SG 3>
> >>>> Added missing heavy atom: .R<FES 268>.A<S3 3>
> >>>> Added missing heavy atom: .R<FES 272>.A<SG 3>
> >>>> Added missing heavy atom: .R<FES 271>.A<SG 3>
> >>>> Added missing heavy atom: .R<FES 269>.A<FE1 1>
> >>>> Added missing heavy atom: .R<FES 270>.A<CB 2>
> >>>> Added missing heavy atom: .R<FES 272>.A<CB 2>
> >>>> Added missing heavy atom: .R<FES 271>.A<CB 2>
> >>>> Added missing heavy atom: .R<FES 269>.A<SG 3>
> >>>> Added missing heavy atom: .R<FES 269>.A<CB 2>
> >>>> Creating new UNIT for residue: CYF sequence: 269
> >>>> Starting new chain with
> >>>> Created a new atom named: N within residue: .R<CYF 269>
> >>>> Created a new atom named: CA within residue: .R<CYF 269>
> >>>> Created a new atom named: C within residue: .R<CYF 269>
> >>>> Created a new atom named: O within residue: .R<CYF 269>
> >>>> Starting new chain with
> >>>> Created a new atom named: FE2 within residue: .R<FES 270>
> >>>> Created a new atom named: CB within residue: .R<FES 270>
> >>>> Created a new atom named: SG within residue: .R<FES 270>
> >>>> Added missing heavy atom: .R<FES 270>.A<S4 4>
> >>>> Added missing heavy atom: .R<FES 272>.A<FE2 1>
> >>>> Added missing heavy atom: .R<FES 274>.A<FE4 1>
> >>>> Added missing heavy atom: .R<FES 273>.A<FE3 1>
> >>>> Added missing heavy atom: .R<FES 270>.A<S1 1>
> >>>> Added missing heavy atom: .R<FES 270>.A<S2 2>
> >>>> Added missing heavy atom: .R<FES 272>.A<SG 3>
> >>>> Added missing heavy atom: .R<FES 270>.A<S3 3>
> >>>> Added missing heavy atom: .R<FES 274>.A<SG 3>
> >>>> Added missing heavy atom: .R<FES 273>.A<SG 3>
> >>>> Added missing heavy atom: .R<FES 271>.A<FE1 1>
> >>>> Added missing heavy atom: .R<FES 272>.A<CB 2>
> >>>> Added missing heavy atom: .R<FES 274>.A<CB 2>
> >>>> Added missing heavy atom: .R<FES 273>.A<CB 2>
> >>>> Added missing heavy atom: .R<FES 271>.A<SG 3>
> >>>> Added missing heavy atom: .R<FES 271>.A<CB 2>
> >>>> Creating new UNIT for residue: CYF sequence: 271
> >>>> Starting new chain with
> >>>> Created a new atom named: N within residue: .R<CYF 271>
> >>>> Created a new atom named: CA within residue: .R<CYF 271>
> >>>> Created a new atom named: C within residue: .R<CYF 271>
> >>>> Created a new atom named: O within residue: .R<CYF 271>
> >>>> Starting new chain with
> >>>> Created a new atom named: FE3 within residue: .R<FES 272>
> >>>> Created a new atom named: CB within residue: .R<FES 272>
> >>>> Created a new atom named: SG within residue: .R<FES 272>
> >>>> Added missing heavy atom: .R<FES 272>.A<S4 4>
> >>>> Added missing heavy atom: .R<FES 274>.A<FE2 1>
> >>>> Added missing heavy atom: .R<FES 276>.A<FE4 1>
> >>>> Added missing heavy atom: .R<FES 275>.A<FE3 1>
> >>>> Added missing heavy atom: .R<FES 272>.A<S1 1>
> >>>> Added missing heavy atom: .R<FES 272>.A<S2 2>
> >>>> Added missing heavy atom: .R<FES 274>.A<SG 3>
> >>>> Added missing heavy atom: .R<FES 272>.A<S3 3>
> >>>> Added missing heavy atom: .R<FES 276>.A<SG 3>
> >>>> Added missing heavy atom: .R<FES 275>.A<SG 3>
> >>>> Added missing heavy atom: .R<FES 273>.A<FE1 1>
> >>>> Added missing heavy atom: .R<FES 274>.A<CB 2>
> >>>> Added missing heavy atom: .R<FES 276>.A<CB 2>
> >>>> Added missing heavy atom: .R<FES 275>.A<CB 2>
> >>>> Added missing heavy atom: .R<FES 273>.A<SG 3>
> >>>> Added missing heavy atom: .R<FES 273>.A<CB 2>
> >>>> Creating new UNIT for residue: CYF sequence: 273
> >>>> Starting new chain with
> >>>> Created a new atom named: N within residue: .R<CYF 273>
> >>>> Created a new atom named: CA within residue: .R<CYF 273>
> >>>> Created a new atom named: C within residue: .R<CYF 273>
> >>>> Created a new atom named: O within residue: .R<CYF 273>
> >>>> Starting new chain with
> >>>> Created a new atom named: FE4 within residue: .R<FES 274>
> >>>> Created a new atom named: CB within residue: .R<FES 274>
> >>>> Created a new atom named: SG within residue: .R<FES 274>
> >>>> Added missing heavy atom: .R<FES 274>.A<S4 4>
> >>>> Added missing heavy atom: .R<FES 276>.A<FE2 1>
> >>>> Added missing heavy atom: .R<FES 278>.A<FE4 1>
> >>>> Added missing heavy atom: .R<FES 277>.A<FE3 1>
> >>>> Added missing heavy atom: .R<FES 274>.A<S1 1>
> >>>> Added missing heavy atom: .R<FES 274>.A<S2 2>
> >>>> Added missing heavy atom: .R<FES 276>.A<SG 3>
> >>>> Added missing heavy atom: .R<FES 274>.A<S3 3>
> >>>> Added missing heavy atom: .R<FES 278>.A<SG 3>
> >>>> Added missing heavy atom: .R<FES 277>.A<SG 3>
> >>>> Added missing heavy atom: .R<FES 275>.A<FE1 1>
> >>>> Added missing heavy atom: .R<FES 276>.A<CB 2>
> >>>> Added missing heavy atom: .R<FES 278>.A<CB 2>
> >>>> Added missing heavy atom: .R<FES 277>.A<CB 2>
> >>>> Added missing heavy atom: .R<FES 275>.A<SG 3>
> >>>> Added missing heavy atom: .R<FES 275>.A<CB 2>
> >>>> Creating new UNIT for residue: CYF sequence: 275
> >>>> Starting new chain with
> >>>> Created a new atom named: N within residue: .R<CYF 275>
> >>>> Created a new atom named: CA within residue: .R<CYF 275>
> >>>> Created a new atom named: C within residue: .R<CYF 275>
> >>>> Created a new atom named: O within residue: .R<CYF 275>
> >>>> total atoms in file: 32
> >>>> Leap added 76 missing atoms according to residue templates:
> >>>> 76 Heavy
> >>>> The file contained 28 atoms not in residue templates
> >>>>> bond x1.268.CB x2.268.CA
> >>>> bond: Argument #2 is type String must be of type: [atom]
> >>>> usage: bond <atom1> <atom2> [order]
> >>>>> bond x1.269.CB x2.269.CA
> >>>> bond: Argument #2 is type String must be of type: [atom]
> >>>> usage: bond <atom1> <atom2> [order]
> >>>>> bond x1.270.CB x2.270.CA
> >>>> bond: Argument #2 is type String must be of type: [atom]
> >>>> usage: bond <atom1> <atom2> [order]
> >>>>> bond x1.271.CB x2.271.CA
> >>>> bond: Argument #2 is type String must be of type: [atom]
> >>>> usage: bond <atom1> <atom2> [order]
> >>>>
> >>>> On 23 Nov 2007, at 18:49, David A. Case wrote:
> >>>>
> >>>>> On Thu, Nov 22, 2007, Bouthe=EFna Kerkeni wrote:
> >>>>>>
> >>>>>>
> >>>>>> Do I need to create 1)a new unit with 4 CA N C O belonging to =20
> >>>>>> modified
> >>>>>> cysteines such that (a made up residue name that is not =20
> >>>>>> currently in use)
> >>>>>> say CY1,CY2 CY3 and CY4? and then bond CYSN.17.CA FES.2.CB etc?
> >>>>>
> >>>>> You probably only need one new residue, not 4. And you would
> >>>>> bond =20=
> >>>
> >>>>> CY1.17.CA
> >>>>> to the cubane, not CYSN.17.CA (what is CYSN?).
> >>>>>
> >>>>> If I understand you corretly.
> >>>>>
> >>>>> I'm not sure how well LEaP will work with residues numbers out of
> >>>>> =20
> >>>>> order (i.e.
> >>>>> residue 20 comes after residue 148.)
> >>>>>
> >>>>> ...dac
> >>>>>
> >>>>
> >>>> ______________________
> >>>> Dr. Boutheina. Kerkeni
> >>>> phone: 02076790486
> >>>> Research Assistant
> >>>> Chemistry Department
> >>>> University College London
> >>>> 20 Gordon Street
> >>>> London
> >>>> WC1H 0AJ
> >>>>
> >>>>
> >>>>
> >>>>
> >>>
> >>> ______________________
> >>> Dr. Boutheina. Kerkeni
> >>> phone: 02076790486
> >>> Research Assistant
> >>> Chemistry Department
> >>> University College London
> >>> 20 Gordon Street
> >>> London
> >>> WC1H 0AJ
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>> ----- End forwarded message -----
> >>>
> >>>
> >>> ----- End forwarded message -----
> >>>
> >>>
> >>> ----- End forwarded message -----
> >>> Now if in the file original.pdb I remove all FES residues/
> >>> ATOM 109 N CYF S 17 31.447 36.047 111.043 1.00
> >>> 2.00 N
> >>> ATOM 110 CA CYF S 17 31.456 37.369 111.671 1.00
> >>> 2.00 C
> >>> ATOM 111 C CYF S 17 32.269 38.354 110.833 1.00
> >>> 2.00 C
> >>> ATOM 112 O CYF S 17 32.279 39.559 111.015 1.00
> >>> 2.00 O
> >>>
> >>> ATOM 805 N CYF S 112 35.516 28.670 112.650 1.00
> >>> 2.00 N
> >>> ATOM 806 CA CYF S 112 34.115 28.402 112.230 1.00
> >>> 2.00 C
> >>> ATOM 807 C CYF S 112 34.090 27.532 110.970 1.00
> >>> 2.00 C
> >>> ATOM 808 O CYF S 112 33.271 26.611 110.929 1.00
> >>> 2.00 O
> >>>
> >>> ATOM 1045 N CYF S 148 40.614 32.189 115.664 1.00
> >>> 2.63 N
> >>> ATOM 1046 CA CYF S 148 39.394 32.998 115.724 1.00
> >>> 2.00 C
> >>> ATOM 1047 C CYF S 148 39.670 34.466 115.933 1.00
> >>> 3.11 C
> >>> ATOM 1048 O CYF S 148 39.313 34.967 117.017 1.00
> >>> 3.02 O
> >>>
> >>> ATOM 126 N CYF S 20 37.429 36.929 109.880 1.00
> >>> 2.00 N
> >>> ATOM 127 CA CYF S 20 38.407 36.075 109.145 1.00
> >>> 2.00 C
> >>> ATOM 128 C CYF S 20 38.867 36.881 107.926 1.00
> >>> 2.00 C
> >>> ATOM 129 O CYF S 20 40.092 36.948 107.685 1.00
> >>> 2.00 O
> >>>
> >>> Xleap creates the bonds as I want, but when I try to create top
> >>> and coord files/
> >>>> saveamberparm x2 x2.prmtop x2.inpcrd
> >>>
> >>> xleap complains about missing bond and angle param/
> >>> N-CA
> >>> N-CA-C
> >>> CA-C-O
> >>>
> >>> should I create a cyf.frcmod fromm amber library? is CM=C? O=OH?
> >>> # modifications to force field for CYF special cysteine
> >>>
> >>> MASS
> >>> N 14.00674
> >>> C 12.0107
> >>> O 15.9994
> >>>
> >>> BOND
> >>> N CA 481.0 1.34
> >>>
> >>> ANGLE
> >>> N CA C 70. 120.1
> >>> CA C O 70. 120.
> >>>
> >>> DIHE
> >>>
> >>> NONB
> >>>
> >>> I have actually tried to do this, and created x2.prmtop and
> >>> x2.inpcrd but the newly formed x2.inpcrd.pdb
> >>> does not contain the cubane!! here it is:
> >>> REMARK
> >>> ATOM 1 N CYF 1 31.447 36.047 111.043
> >>> ATOM 2 CA CYF 1 31.456 37.369 111.671
> >>> ATOM 3 C CYF 1 32.269 38.354 110.833
> >>> ATOM 4 O CYF 1 32.279 39.559 111.015
> >>> TER
> >>> ATOM 5 N CYF 2 35.516 28.670 112.650
> >>> ATOM 6 CA CYF 2 34.115 28.402 112.230
> >>> ATOM 7 C CYF 2 34.090 27.532 110.970
> >>> ATOM 8 O CYF 2 33.271 26.611 110.929
> >>> TER
> >>> ATOM 9 N CYF 3 40.614 32.189 115.664
> >>> ATOM 10 CA CYF 3 39.394 32.998 115.724
> >>> ATOM 11 C CYF 3 39.670 34.466 115.933
> >>> ATOM 12 O CYF 3 39.313 34.967 117.017
> >>> TER
> >>> ATOM 13 N CYF 4 37.429 36.929 109.880
> >>> ATOM 14 CA CYF 4 38.407 36.075 109.145
> >>> ATOM 15 C CYF 4 38.867 36.881 107.926
> >>> ATOM 16 O CYF 4 40.092 36.948 107.685
> >>> TER
> >>> END
> >>>
> >>> I am really very confused now, I have been working on this bit all
> >>> week!!! I am hence out of my wits.
> >>> Any help is very much appreciated.
> >>> Regards
> >>> Begin forwarded message:
> >>>
> >>>> From: Boutheïna Kerkeni <b.kerkeni.ucl.ac.uk>
> >>>> Date: 23 November 2007 19:24:43 GMT
> >>>> To: David A. Case <case.scripps.edu>
> >>>> Subject: Re: AMBER: modifications to force field for Fe4S4 cubane
> >>>>
> >>>> I have tryied to use the bond command but xleap complained:
> >>>> (details are below:)
> >>>>
> >>>>> bond x1.268.CB x2.268.CA
> >>>> bond: Argument #2 is type String must be of type: [atom]
> >>>> usage: bond <atom1> <atom2> [order]
> >>>>> bond x1.269.CB x2.269.CA
> >>>> bond: Argument #2 is type String must be of type: [atom]
> >>>> usage: bond <atom1> <atom2> [order]
> >>>>> bond x1.270.CB x2.270.CA
> >>>> bond: Argument #2 is type String must be of type: [atom]
> >>>> usage: bond <atom1> <atom2> [order]
> >>>>> bond x1.271.CB x2.271.CA
> >>>> bond: Argument #2 is type String must be of type: [atom]
> >>>> usage: bond <atom1> <atom2> [order]
> >>>>
> >>>> This is my fes.pdb
> >>>> HETATM 1985 S1 FES S 267 34.447 34.094 111.212 1.00
> >>>> 2.00 S
> >>>> HETATM 1986 S2 FES S 267 33.848 33.897 114.767 1.00
> >>>> 2.00 S
> >>>> HETATM 1987 S3 FES S 267 36.832 35.519 113.511 1.00
> >>>> 2.00 S
> >>>> HETATM 1988 S4 FES S 267 36.543 31.924 113.185 1.00
> >>>> 2.00 S
> >>>>
> >>>> HETATM 1981 FE1 FES S 17 34.634 35.304 113.224 1.00
> >>>> 2.00 FE
> >>>> ATOM 113 CB FES S 17 31.984 37.285 113.115 1.00
> >>>> 2.00 C
> >>>> ATOM 114 SG FES S 17 33.787 37.364 113.280 1.00
> >>>> 2.00 S
> >>>>
> >>>> HETATM 1982 FE2 FES S 112 34.363 32.588 112.931 1.00
> >>>> 2.00 FE
> >>>> ATOM 809 CB FES S 112 33.352 29.697 112.009 1.00
> >>>> 2.00 C
> >>>> ATOM 810 SG FES S 112 33.038 30.838 113.289 1.00
> >>>> 2.00 S
> >>>>
> >>>> HETATM 1983 FE3 FES S 148 36.083 33.652 114.690 1.00
> >>>> 2.76 FE
> >>>> ATOM 1049 CB FES S 148 38.546 32.478 116.891 1.00
> >>>> 2.00 C
> >>>> ATOM 1050 SG FES S 148 36.839 33.007 116.844 1.00
> >>>> 2.00 S
> >>>>
> >>>> HETATM 1984 FE4 FES S 20 36.595 33.848 111.968 1.00
> >>>> 2.00 FE
> >>>> ATOM 130 CB FES S 20 37.983 34.648 108.903 1.00
> >>>> 2.00 C
> >>>> ATOM 131 SG FES S 20 38.200 33.520 110.342 1.00
> >>>> 2.00 S
> >>>>
> >>>> to which I created FES.lib (after adding charges, and loading
> >>>> the .frcmod file to xleap)
> >>>>
> >>>> This is my modified(creation of 4 CYF residues) initial pdb file
> >>>> (cut out from the enzyme)
> >>>> file.pdb
> >>>> HETATM 1985 S1 FES S 267 34.447 34.094 111.212 1.00
> >>>> 2.00 S
> >>>> HETATM 1986 S2 FES S 267 33.848 33.897 114.767 1.00
> >>>> 2.00 S
> >>>> HETATM 1987 S3 FES S 267 36.832 35.519 113.511 1.00
> >>>> 2.00 S
> >>>> HETATM 1988 S4 FES S 267 36.543 31.924 113.185 1.00
> >>>> 2.00 S
> >>>>
> >>>> HETATM 1981 FE1 FES S 17 34.634 35.304 113.224 1.00
> >>>> 2.00 FE
> >>>> ATOM 113 CB FES S 17 31.984 37.285 113.115 1.00
> >>>> 2.00 C
> >>>> ATOM 114 SG FES S 17 33.787 37.364 113.280 1.00
> >>>> 2.00 S
> >>>> ATOM 109 N CYF S 17 31.447 36.047 111.043 1.00
> >>>> 2.00 N
> >>>> ATOM 110 CA CYF S 17 31.456 37.369 111.671 1.00
> >>>> 2.00 C
> >>>> ATOM 111 C CYF S 17 32.269 38.354 110.833 1.00
> >>>> 2.00 C
> >>>> ATOM 112 O CYF S 17 32.279 39.559 111.015 1.00
> >>>> 2.00 O
> >>>>
> >>>> HETATM 1982 FE2 FES S 112 34.363 32.588 112.931 1.00
> >>>> 2.00 FE
> >>>> ATOM 809 CB FES S 112 33.352 29.697 112.009 1.00
> >>>> 2.00 C
> >>>> ATOM 810 SG FES S 112 33.038 30.838 113.289 1.00
> >>>> 2.00 S
> >>>> ATOM 805 N CYF S 112 35.516 28.670 112.650 1.00
> >>>> 2.00 N
> >>>> ATOM 806 CA CYF S 112 34.115 28.402 112.230 1.00
> >>>> 2.00 C
> >>>> ATOM 807 C CYF S 112 34.090 27.532 110.970 1.00
> >>>> 2.00 C
> >>>> ATOM 808 O CYF S 112 33.271 26.611 110.929 1.00
> >>>> 2.00 O
> >>>>
> >>>> HETATM 1983 FE3 FES S 148 36.083 33.652 114.690 1.00
> >>>> 2.76 FE
> >>>> ATOM 1049 CB FES S 148 38.546 32.478 116.891 1.00
> >>>> 2.00 C
> >>>> ATOM 1050 SG FES S 148 36.839 33.007 116.844 1.00
> >>>> 2.00 S
> >>>> ATOM 1045 N CYF S 148 40.614 32.189 115.664 1.00
> >>>> 2.63 N
> >>>> ATOM 1046 CA CYF S 148 39.394 32.998 115.724 1.00
> >>>> 2.00 C
> >>>> ATOM 1047 C CYF S 148 39.670 34.466 115.933 1.00
> >>>> 3.11 C
> >>>> ATOM 1048 O CYF S 148 39.313 34.967 117.017 1.00
> >>>> 3.02 O
> >>>>
> >>>> HETATM 1984 FE4 FES S 20 36.595 33.848 111.968 1.00
> >>>> 2.00 FE
> >>>> ATOM 130 CB FES S 20 37.983 34.648 108.903 1.00
> >>>> 2.00 C
> >>>> ATOM 131 SG FES S 20 38.200 33.520 110.342 1.00
> >>>> 2.00 S
> >>>> ATOM 126 N CYF S 20 37.429 36.929 109.880 1.00
> >>>> 2.00 N
> >>>> ATOM 127 CA CYF S 20 38.407 36.075 109.145 1.00
> >>>> 2.00 C
> >>>> ATOM 128 C CYF S 20 38.867 36.881 107.926 1.00
> >>>> 2.00 C
> >>>> ATOM 129 O CYF S 20 40.092 36.948 107.685 1.00
> >>>> 2.00 O
> >>>>
> >>>> In xleap I did:
> >>>>> loadoff FES.lib
> >>>>> x1=loadpdb fes.pdb
> >>>> Loading PDB file: ./fes.pdb
> >>>> Enter zPdbReadScan from call depth 0.
> >>>> Exit zPdbReadScan from call depth 0.
> >>>> Matching PDB residue names to LEaP variables.
> >>>> (Residue 0: FES, Terminal/beginning, was not found in name map.)
> >>>> (Residue 1: FES, Nonterminal, was not found in name map.)
> >>>> (Residue 2: FES, Nonterminal, was not found in name map.)
> >>>> (Residue 3: FES, Nonterminal, was not found in name map.)
> >>>> (Residue 4: FES, Terminal/last, was not found in name map.)
> >>>> Added missing heavy atom: .R<FES 269>.A<FE2 1>
> >>>> Added missing heavy atom: .R<FES 269>.A<SG 3>
> >>>> Added missing heavy atom: .R<FES 269>.A<CB 2>
> >>>> Added missing heavy atom: .R<FES 271>.A<FE4 1>
> >>>> Added missing heavy atom: .R<FES 271>.A<SG 3>
> >>>> Added missing heavy atom: .R<FES 271>.A<CB 2>
> >>>> Added missing heavy atom: .R<FES 270>.A<FE3 1>
> >>>> Added missing heavy atom: .R<FES 270>.A<SG 3>
> >>>> Added missing heavy atom: .R<FES 270>.A<CB 2>
> >>>> Added missing heavy atom: .R<FES 268>.A<FE1 1>
> >>>> Added missing heavy atom: .R<FES 268>.A<SG 3>
> >>>> Added missing heavy atom: .R<FES 268>.A<CB 2>
> >>>> Starting new chain with
> >>>> Created a new atom named: FE1 within residue: .R<FES 268>
> >>>> Created a new atom named: CB within residue: .R<FES 268>
> >>>> Created a new atom named: SG within residue: .R<FES 268>
> >>>> Added missing heavy atom: .R<FES 268>.A<S4 4>
> >>>> Added missing heavy atom: .R<FES 270>.A<FE2 1>
> >>>> Added missing heavy atom: .R<FES 272>.A<FE4 1>
> >>>> Added missing heavy atom: .R<FES 271>.A<FE3 1>
> >>>> Added missing heavy atom: .R<FES 268>.A<S1 1>
> >>>> Added missing heavy atom: .R<FES 268>.A<S2 2>
> >>>> Added missing heavy atom: .R<FES 270>.A<SG 3>
> >>>> Added missing heavy atom: .R<FES 268>.A<S3 3>
> >>>> Added missing heavy atom: .R<FES 272>.A<SG 3>
> >>>> Added missing heavy atom: .R<FES 271>.A<SG 3>
> >>>> Added missing heavy atom: .R<FES 269>.A<FE1 1>
> >>>> Added missing heavy atom: .R<FES 270>.A<CB 2>
> >>>> Added missing heavy atom: .R<FES 272>.A<CB 2>
> >>>> Added missing heavy atom: .R<FES 271>.A<CB 2>
> >>>> Added missing heavy atom: .R<FES 269>.A<SG 3>
> >>>> Added missing heavy atom: .R<FES 269>.A<CB 2>
> >>>> Starting new chain with
> >>>> Created a new atom named: FE2 within residue: .R<FES 269>
> >>>> Created a new atom named: CB within residue: .R<FES 269>
> >>>> Created a new atom named: SG within residue: .R<FES 269>
> >>>> Added missing heavy atom: .R<FES 269>.A<S4 4>
> >>>> Added missing heavy atom: .R<FES 271>.A<FE2 1>
> >>>> Added missing heavy atom: .R<FES 273>.A<FE4 1>
> >>>> Added missing heavy atom: .R<FES 272>.A<FE3 1>
> >>>> Added missing heavy atom: .R<FES 269>.A<S1 1>
> >>>> Added missing heavy atom: .R<FES 269>.A<S2 2>
> >>>> Added missing heavy atom: .R<FES 271>.A<SG 3>
> >>>> Added missing heavy atom: .R<FES 269>.A<S3 3>
> >>>> Added missing heavy atom: .R<FES 273>.A<SG 3>
> >>>> Added missing heavy atom: .R<FES 272>.A<SG 3>
> >>>> Added missing heavy atom: .R<FES 270>.A<FE1 1>
> >>>> Added missing heavy atom: .R<FES 271>.A<CB 2>
> >>>> Added missing heavy atom: .R<FES 273>.A<CB 2>
> >>>> Added missing heavy atom: .R<FES 272>.A<CB 2>
> >>>> Added missing heavy atom: .R<FES 270>.A<SG 3>
> >>>> Added missing heavy atom: .R<FES 270>.A<CB 2>
> >>>> Starting new chain with
> >>>> Created a new atom named: FE3 within residue: .R<FES 270>
> >>>> Created a new atom named: CB within residue: .R<FES 270>
> >>>> Created a new atom named: SG within residue: .R<FES 270>
> >>>> Added missing heavy atom: .R<FES 270>.A<S4 4>
> >>>> Added missing heavy atom: .R<FES 272>.A<FE2 1>
> >>>> Added missing heavy atom: .R<FES 274>.A<FE4 1>
> >>>> Added missing heavy atom: .R<FES 273>.A<FE3 1>
> >>>> Added missing heavy atom: .R<FES 270>.A<S1 1>
> >>>> Added missing heavy atom: .R<FES 270>.A<S2 2>
> >>>> Added missing heavy atom: .R<FES 272>.A<SG 3>
> >>>> Added missing heavy atom: .R<FES 270>.A<S3 3>
> >>>> Added missing heavy atom: .R<FES 274>.A<SG 3>
> >>>> Added missing heavy atom: .R<FES 273>.A<SG 3>
> >>>> Added missing heavy atom: .R<FES 271>.A<FE1 1>
> >>>> Added missing heavy atom: .R<FES 272>.A<CB 2>
> >>>> Added missing heavy atom: .R<FES 274>.A<CB 2>
> >>>> Added missing heavy atom: .R<FES 273>.A<CB 2>
> >>>> Added missing heavy atom: .R<FES 271>.A<SG 3>
> >>>> Added missing heavy atom: .R<FES 271>.A<CB 2>
> >>>> Starting new chain with
> >>>> Created a new atom named: FE4 within residue: .R<FES 271>
> >>>> Created a new atom named: CB within residue: .R<FES 271>
> >>>> Created a new atom named: SG within residue: .R<FES 271>
> >>>> Added missing heavy atom: .R<FES 271>.A<S4 4>
> >>>> Added missing heavy atom: .R<FES 273>.A<FE2 1>
> >>>> Added missing heavy atom: .R<FES 275>.A<FE4 1>
> >>>> Added missing heavy atom: .R<FES 274>.A<FE3 1>
> >>>> Added missing heavy atom: .R<FES 271>.A<S1 1>
> >>>> Added missing heavy atom: .R<FES 271>.A<S2 2>
> >>>> Added missing heavy atom: .R<FES 273>.A<SG 3>
> >>>> Added missing heavy atom: .R<FES 271>.A<S3 3>
> >>>> Added missing heavy atom: .R<FES 275>.A<SG 3>
> >>>> Added missing heavy atom: .R<FES 274>.A<SG 3>
> >>>> Added missing heavy atom: .R<FES 272>.A<FE1 1>
> >>>> Added missing heavy atom: .R<FES 273>.A<CB 2>
> >>>> Added missing heavy atom: .R<FES 275>.A<CB 2>
> >>>> Added missing heavy atom: .R<FES 274>.A<CB 2>
> >>>> Added missing heavy atom: .R<FES 272>.A<SG 3>
> >>>> Added missing heavy atom: .R<FES 272>.A<CB 2>
> >>>> total atoms in file: 16
> >>>> Leap added 76 missing atoms according to residue templates:
> >>>> 76 Heavy
> >>>> The file contained 12 atoms not in residue templates
> >>>>
> >>>>> x2=loadpdb original.pdb
> >>>>> x2=loadpdb original.pdb
> >>>> Loading PDB file: ./original.pdb
> >>>> Enter zPdbReadScan from call depth 0.
> >>>> Warning: name change in pdb file residue 17 ;
> >>>> this residue is split into FES and CYF.
> >>>> Warning: name change in pdb file residue 112 ;
> >>>> this residue is split into FES and CYF.
> >>>> Warning: name change in pdb file residue 148 ;
> >>>> this residue is split into FES and CYF.
> >>>> Warning: name change in pdb file residue 20 ;
> >>>> this residue is split into FES and CYF.
> >>>> 4 residues had naming warnings.
> >>>> There are split residues;
> >>>> residue sequence numbers will not correspond to those in the pdb.
> >>>> Exit zPdbReadScan from call depth 0.
> >>>> Matching PDB residue names to LEaP variables.
> >>>> (Residue 0: FES, Terminal/beginning, was not found in name map.)
> >>>> (Residue 1: FES, Nonterminal, was not found in name map.)
> >>>> (Residue 2: CYF, Nonterminal, was not found in name map.)
> >>>> Unknown residue: CYF number: 2 type: Nonterminal
> >>>> (Residue 3: FES, Nonterminal, was not found in name map.)
> >>>> (Residue 4: CYF, Nonterminal, was not found in name map.)
> >>>> Unknown residue: CYF number: 4 type: Nonterminal
> >>>> (Residue 5: FES, Nonterminal, was not found in name map.)
> >>>> (Residue 6: CYF, Nonterminal, was not found in name map.)
> >>>> Unknown residue: CYF number: 6 type: Nonterminal
> >>>> (Residue 7: FES, Nonterminal, was not found in name map.)
> >>>> (Residue 8: CYF, Terminal/last, was not found in name map.)
> >>>> Unknown residue: CYF number: 8 type: Terminal/last
> >>>> ..relaxing end constraints to try for a dbase match
> >>>> -no luck
> >>>> Added missing heavy atom: .R<FES 269>.A<FE2 1>
> >>>> Added missing heavy atom: .R<FES 269>.A<SG 3>
> >>>> Added missing heavy atom: .R<FES 269>.A<CB 2>
> >>>> Added missing heavy atom: .R<FES 271>.A<FE4 1>
> >>>> Added missing heavy atom: .R<FES 271>.A<SG 3>
> >>>> Added missing heavy atom: .R<FES 271>.A<CB 2>
> >>>> Added missing heavy atom: .R<FES 270>.A<FE3 1>
> >>>> Added missing heavy atom: .R<FES 270>.A<SG 3>
> >>>> Added missing heavy atom: .R<FES 270>.A<CB 2>
> >>>> Added missing heavy atom: .R<FES 268>.A<FE1 1>
> >>>> Added missing heavy atom: .R<FES 268>.A<SG 3>
> >>>> Added missing heavy atom: .R<FES 268>.A<CB 2>
> >>>> Starting new chain with
> >>>> Created a new atom named: FE1 within residue: .R<FES 268>
> >>>> Created a new atom named: CB within residue: .R<FES 268>
> >>>> Created a new atom named: SG within residue: .R<FES 268>
> >>>> Added missing heavy atom: .R<FES 268>.A<S4 4>
> >>>> Added missing heavy atom: .R<FES 270>.A<FE2 1>
> >>>> Added missing heavy atom: .R<FES 272>.A<FE4 1>
> >>>> Added missing heavy atom: .R<FES 271>.A<FE3 1>
> >>>> Added missing heavy atom: .R<FES 268>.A<S1 1>
> >>>> Added missing heavy atom: .R<FES 268>.A<S2 2>
> >>>> Added missing heavy atom: .R<FES 270>.A<SG 3>
> >>>> Added missing heavy atom: .R<FES 268>.A<S3 3>
> >>>> Added missing heavy atom: .R<FES 272>.A<SG 3>
> >>>> Added missing heavy atom: .R<FES 271>.A<SG 3>
> >>>> Added missing heavy atom: .R<FES 269>.A<FE1 1>
> >>>> Added missing heavy atom: .R<FES 270>.A<CB 2>
> >>>> Added missing heavy atom: .R<FES 272>.A<CB 2>
> >>>> Added missing heavy atom: .R<FES 271>.A<CB 2>
> >>>> Added missing heavy atom: .R<FES 269>.A<SG 3>
> >>>> Added missing heavy atom: .R<FES 269>.A<CB 2>
> >>>> Creating new UNIT for residue: CYF sequence: 269
> >>>> Starting new chain with
> >>>> Created a new atom named: N within residue: .R<CYF 269>
> >>>> Created a new atom named: CA within residue: .R<CYF 269>
> >>>> Created a new atom named: C within residue: .R<CYF 269>
> >>>> Created a new atom named: O within residue: .R<CYF 269>
> >>>> Starting new chain with
> >>>> Created a new atom named: FE2 within residue: .R<FES 270>
> >>>> Created a new atom named: CB within residue: .R<FES 270>
> >>>> Created a new atom named: SG within residue: .R<FES 270>
> >>>> Added missing heavy atom: .R<FES 270>.A<S4 4>
> >>>> Added missing heavy atom: .R<FES 272>.A<FE2 1>
> >>>> Added missing heavy atom: .R<FES 274>.A<FE4 1>
> >>>> Added missing heavy atom: .R<FES 273>.A<FE3 1>
> >>>> Added missing heavy atom: .R<FES 270>.A<S1 1>
> >>>> Added missing heavy atom: .R<FES 270>.A<S2 2>
> >>>> Added missing heavy atom: .R<FES 272>.A<SG 3>
> >>>> Added missing heavy atom: .R<FES 270>.A<S3 3>
> >>>> Added missing heavy atom: .R<FES 274>.A<SG 3>
> >>>> Added missing heavy atom: .R<FES 273>.A<SG 3>
> >>>> Added missing heavy atom: .R<FES 271>.A<FE1 1>
> >>>> Added missing heavy atom: .R<FES 272>.A<CB 2>
> >>>> Added missing heavy atom: .R<FES 274>.A<CB 2>
> >>>> Added missing heavy atom: .R<FES 273>.A<CB 2>
> >>>> Added missing heavy atom: .R<FES 271>.A<SG 3>
> >>>> Added missing heavy atom: .R<FES 271>.A<CB 2>
> >>>> Creating new UNIT for residue: CYF sequence: 271
> >>>> Starting new chain with
> >>>> Created a new atom named: N within residue: .R<CYF 271>
> >>>> Created a new atom named: CA within residue: .R<CYF 271>
> >>>> Created a new atom named: C within residue: .R<CYF 271>
> >>>> Created a new atom named: O within residue: .R<CYF 271>
> >>>> Starting new chain with
> >>>> Created a new atom named: FE3 within residue: .R<FES 272>
> >>>> Created a new atom named: CB within residue: .R<FES 272>
> >>>> Created a new atom named: SG within residue: .R<FES 272>
> >>>> Added missing heavy atom: .R<FES 272>.A<S4 4>
> >>>> Added missing heavy atom: .R<FES 274>.A<FE2 1>
> >>>> Added missing heavy atom: .R<FES 276>.A<FE4 1>
> >>>> Added missing heavy atom: .R<FES 275>.A<FE3 1>
> >>>> Added missing heavy atom: .R<FES 272>.A<S1 1>
> >>>> Added missing heavy atom: .R<FES 272>.A<S2 2>
> >>>> Added missing heavy atom: .R<FES 274>.A<SG 3>
> >>>> Added missing heavy atom: .R<FES 272>.A<S3 3>
> >>>> Added missing heavy atom: .R<FES 276>.A<SG 3>
> >>>> Added missing heavy atom: .R<FES 275>.A<SG 3>
> >>>> Added missing heavy atom: .R<FES 273>.A<FE1 1>
> >>>> Added missing heavy atom: .R<FES 274>.A<CB 2>
> >>>> Added missing heavy atom: .R<FES 276>.A<CB 2>
> >>>> Added missing heavy atom: .R<FES 275>.A<CB 2>
> >>>> Added missing heavy atom: .R<FES 273>.A<SG 3>
> >>>> Added missing heavy atom: .R<FES 273>.A<CB 2>
> >>>> Creating new UNIT for residue: CYF sequence: 273
> >>>> Starting new chain with
> >>>> Created a new atom named: N within residue: .R<CYF 273>
> >>>> Created a new atom named: CA within residue: .R<CYF 273>
> >>>> Created a new atom named: C within residue: .R<CYF 273>
> >>>> Created a new atom named: O within residue: .R<CYF 273>
> >>>> Starting new chain with
> >>>> Created a new atom named: FE4 within residue: .R<FES 274>
> >>>> Created a new atom named: CB within residue: .R<FES 274>
> >>>> Created a new atom named: SG within residue: .R<FES 274>
> >>>> Added missing heavy atom: .R<FES 274>.A<S4 4>
> >>>> Added missing heavy atom: .R<FES 276>.A<FE2 1>
> >>>> Added missing heavy atom: .R<FES 278>.A<FE4 1>
> >>>> Added missing heavy atom: .R<FES 277>.A<FE3 1>
> >>>> Added missing heavy atom: .R<FES 274>.A<S1 1>
> >>>> Added missing heavy atom: .R<FES 274>.A<S2 2>
> >>>> Added missing heavy atom: .R<FES 276>.A<SG 3>
> >>>> Added missing heavy atom: .R<FES 274>.A<S3 3>
> >>>> Added missing heavy atom: .R<FES 278>.A<SG 3>
> >>>> Added missing heavy atom: .R<FES 277>.A<SG 3>
> >>>> Added missing heavy atom: .R<FES 275>.A<FE1 1>
> >>>> Added missing heavy atom: .R<FES 276>.A<CB 2>
> >>>> Added missing heavy atom: .R<FES 278>.A<CB 2>
> >>>> Added missing heavy atom: .R<FES 277>.A<CB 2>
> >>>> Added missing heavy atom: .R<FES 275>.A<SG 3>
> >>>> Added missing heavy atom: .R<FES 275>.A<CB 2>
> >>>> Creating new UNIT for residue: CYF sequence: 275
> >>>> Starting new chain with
> >>>> Created a new atom named: N within residue: .R<CYF 275>
> >>>> Created a new atom named: CA within residue: .R<CYF 275>
> >>>> Created a new atom named: C within residue: .R<CYF 275>
> >>>> Created a new atom named: O within residue: .R<CYF 275>
> >>>> total atoms in file: 32
> >>>> Leap added 76 missing atoms according to residue templates:
> >>>> 76 Heavy
> >>>> The file contained 28 atoms not in residue templates
> >>>>> bond x1.268.CB x2.268.CA
> >>>> bond: Argument #2 is type String must be of type: [atom]
> >>>> usage: bond <atom1> <atom2> [order]
> >>>>> bond x1.269.CB x2.269.CA
> >>>> bond: Argument #2 is type String must be of type: [atom]
> >>>> usage: bond <atom1> <atom2> [order]
> >>>>> bond x1.270.CB x2.270.CA
> >>>> bond: Argument #2 is type String must be of type: [atom]
> >>>> usage: bond <atom1> <atom2> [order]
> >>>>> bond x1.271.CB x2.271.CA
> >>>> bond: Argument #2 is type String must be of type: [atom]
> >>>> usage: bond <atom1> <atom2> [order]
> >>>>
> >>>> On 23 Nov 2007, at 18:49, David A. Case wrote:
> >>>>
> >>>>> On Thu, Nov 22, 2007, Boutheïna Kerkeni wrote:
> >>>>>>
> >>>>>>
> >>>>>> Do I need to create 1)a new unit with 4 CA N C O belonging to
> >>>>>> modified
> >>>>>> cysteines such that (a made up residue name that is not
> >>>>>> currently in use)
> >>>>>> say CY1,CY2 CY3 and CY4? and then bond CYSN.17.CA FES.2.CB etc?
> >>>>>
> >>>>> You probably only need one new residue, not 4. And you would
> >>>>> bond CY1.17.CA
> >>>>> to the cubane, not CYSN.17.CA (what is CYSN?).
> >>>>>
> >>>>> If I understand you corretly.
> >>>>>
> >>>>> I'm not sure how well LEaP will work with residues numbers out of
> >>>>> order (i.e.
> >>>>> residue 20 comes after residue 148.)
> >>>>>
> >>>>> ...dac
> >>>>>
> >>
> >
> > --
> > Ilyas Yildirim
> > ---------------------------------------------------------------
> > = Department of Chemistry - =
> > = University of Rochester - =
> > = Rochester, NY 14627-0216 - Ph.:(585) 275 67 66 (Office) =
> > = http://www.pas.rochester.edu/~yildirim/ =
> > ---------------------------------------------------------------
> >
> > ----------------------------------------------------------------------
> > -
> > The AMBER Mail Reflector
> > To post, send mail to amber.scripps.edu
> > To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
> ______________________
> Dr. Boutheina. Kerkeni
> phone: 02076790486
> Research Assistant
> Chemistry Department
> University College London
> 20 Gordon Street
> London
> WC1H 0AJ
>
>
>
>
>

-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
  = Department of Chemistry      -                              =
  = University of Rochester      -                              =
  = Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office) =
  = http://www.pas.rochester.edu/~yildirim/                     =
  ---------------------------------------------------------------
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu

Received on Wed Nov 28 2007 - 06:07:39 PST