Re: AMBER: modifications to force field for Fe4S4 cubane

From: Ilyas Yildirim <yildirim.pas.rochester.edu>
Date: Tue, 27 Nov 2007 10:02:21 -0500 (EST)

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, Bouthe´na 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: Bouthe´na 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, Bouthe´na 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/                     =
  ---------------------------------------------------------------
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Received on Wed Nov 28 2007 - 06:07:35 PST
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