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
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______________________
Dr. Boutheina. Kerkeni
phone: 02076790486
Research Assistant
Chemistry Department
University College London
20 Gordon Street
London
WC1H 0AJ
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Received on Wed Nov 28 2007 - 06:07:35 PST
