AMBER Archive (2007)

Subject: AMBER: modifications to force field for Fe4S4 cubane

From: Boutheïna Kerkeni (b.kerkeni_at_ucl.ac.uk)
Date: Tue Nov 27 2007 - 05:26:22 CST

>
> 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_at_ucl.ac.uk>
>> Date: 23 November 2007 19:24:43 GMT
>> To: David A. Case <case_at_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_at_ucl.ac.uk>
>> Date: 23 November 2007 19:24:43 GMT
>> To: David A. Case <case_at_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
>>>
  
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