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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
*

*>
*

*>
*

*>
*

*>
*

*>
*

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:

-- 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.eduReceived on Wed Nov 28 2007 - 06:07:39 PST

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