AMBER: modifications to force field for Fe4S4 cubane

From: Bouthe´na Kerkeni <b.kerkeni.ucl.ac.uk>
Date: Wed, 21 Nov 2007 21:41:45 +0000

Dear Amber users

I am a new user of Amber. Please could you help with the following
problems?
Thanks very much in advance

1)The first problem I encountered is that my newly created pdb from
frcmod file, when visualzed in VMD is completely disconnected no
bonds between atoms! Is this normal?
2) The second being: how to connect the CB(CT) carbons to CA (ie the
rest of the 4 CYS of this cubane)??


I am trying to generate parameters for the Fe4S4 cubane cluster that
is found in an enzyme.
I have created a frcmod file: fe4s4c.frcmod
# modifications to force field for Fe4S4 cubane

MASS
S2 32.066
FE 55.845

BOND
FE SH 83.947 2.282
FE S2 61.467 2.307

ANGLE
SH FE S2 30.053 111.97
FE SH CT 64.577 99.98
S2 FE S2 27.483 106.86
FE S2 FE 31.210 69.85

DIHE
S2 FE SH CT 1 0.00 0.00 3. ! 23.01 3 1
SH FE S2 FE 1 0.00 180.00 6. ! 24.42 3 2
FE SH CT H1 1 0.00 0.00 3. ! 20.32 1 3
S2 FE S2 FE 1 0.00 0.00 6. ! 25.23 3 2

NONB
S2 2.0000 0.2500
FE 0.0100 0.6500

I have cut out from the enzyme pdb file the cubane cluster with only
the SG carbons (hence without the entire CYS) (FES.pdb), after
modifications (i.e FES residue name) it looks like

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


Now, I have edited the file in xleap and created atom types and
inserted charges, I gain a lib file FES.lib

!!index array str
  "FES"
!entry.FES.unit.atoms table str name str type int typex int resx
int flags int seq
  int elmnt dbl chg
  "S1" "S2" 0 1 131075 1 16 -0.381660
  "S2" "S2" 0 1 131075 2 16 -0.232370
  "S3" "S2" 0 1 131075 3 16 -0.328940
  "S4" "S2" 0 1 131075 4 16 -0.268610
  "FE1" "FE" 0 2 131075 1 26 0.246580
  "CB" "CT" 0 2 131075 2 6 0.120765
  "SG" "SH" 0 2 131075 3 16 -0.594340
  "FE2" "FE" 0 3 131075 1 26 0.256830
  "CB" "CT" 0 3 131075 2 6 0.120765
  "SG" "SH" 0 3 131075 3 16 -0.656520
  "FE3" "FE" 0 4 131075 1 26 0.318960
  "CB" "CT" 0 4 131075 2 6 0.120765
  "SG" "SH" 0 4 131075 3 16 -0.588970
  "FE4" "FE" 0 5 131075 1 26 0.324580
  "CB" "CT" 0 5 131075 2 6 0.120765
  "SG" "SH" 0 5 131075 3 16 -0.578600
!entry.FES.unit.atomspertinfo table str pname str ptype int
ptypex int pelmnt dbl pc
hg
  "S1" "S2" 0 -1 0.0
  "S2" "S2" 0 -1 0.0
  "S3" "S2" 0 -1 0.0
  "S4" "S2" 0 -1 0.0
  "FE1" "FE" 0 -1 0.0
  "CB" "CT" 0 -1 0.0
  "SG" "SH" 0 -1 0.0
  "FE2" "FE" 0 -1 0.0
  "CB" "CT" 0 -1 0.0
  "SG" "SH" 0 -1 0.0
  "FE3" "FE" 0 -1 0.0
  "CB" "CT" 0 -1 0.0
  "SG" "SH" 0 -1 0.0
  "FE4" "FE" 0 -1 0.0
  "CB" "CT" 0 -1 0.0
  "SG" "SH" 0 -1 0.0
!entry.FES.unit.boundbox array dbl
  -1.000000
  0.0
  0.0
  0.0
  0.0
!entry.FES.unit.childsequence single int
  272
!entry.FES.unit.connect array int
  0
  0
!entry.FES.unit.connectivity table int atom1x int atom2x int flags
  1 14 1
  1 8 1
  1 5 1
  2 8 1
  2 5 1
  2 11 1
  3 5 1
  3 11 1
  3 14 1
  4 8 1
  4 14 1
  4 11 1
  5 7 1
  6 7 1
  8 10 1
  9 10 1
  11 13 1
  12 13 1
  14 16 1
  15 16 1
!entry.FES.unit.hierarchy table str abovetype int abovex str
belowtype int belowx
  "U" 0 "R" 1
  "R" 1 "A" 1
  "R" 1 "A" 2
  "R" 1 "A" 3
  "R" 1 "A" 4
  "U" 0 "R" 2
  "R" 2 "A" 5
  "R" 2 "A" 6
  "R" 2 "A" 7
  "U" 0 "R" 3
  "R" 3 "A" 8
  "R" 3 "A" 9
  "R" 3 "A" 10
  "U" 0 "R" 4
  "R" 4 "A" 11
  "R" 4 "A" 12
  "R" 4 "A" 13
  "U" 0 "R" 5
  "R" 5 "A" 14
  "R" 5 "A" 15
  "R" 5 "A" 16
!entry.FES.unit.name single str
  ""
!entry.FES.unit.positions table dbl x dbl y dbl z
  34.447000 34.094000 111.212000
  33.848000 33.897000 114.767000
  36.832000 35.519000 113.511000
  36.543000 31.924000 113.185000
  34.634000 35.304000 113.224000
31.984000 37.285000 113.115000
  33.787000 37.364000 113.280000
  34.363000 32.588000 112.931000
  33.352000 29.697000 112.009000
  33.038000 30.838000 113.289000
  36.083000 33.652000 114.690000
  38.546000 32.478000 116.891000
  36.839000 33.007000 116.844000
  36.595000 33.848000 111.968000
  37.983000 34.648000 108.903000
  38.200000 33.520000 110.342000
!entry.FES.unit.residueconnect table int c1x int c2x int c3x int
c4x int c5x int c6
x
  0 0 0 0 0 0
  0 0 0 0 0 0
  0 0 0 0 0 0
  0 0 0 0 0 0
  0 0 0 0 0 0
!entry.FES.unit.residues table str name int seq int childseq int
startatomx str rest
ype int imagingx
  "FES" 267 5 1 "?" 0
  "FES" 268 4 5 "?" 0
  "FES" 269 4 8 "?" 0
  "FES" 270 4 11 "?" 0
  "FES" 271 4 14 "?" 0
!entry.FES.unit.residuesPdbSequenceNumber array int
  1
  2
  3
  4
  5
!entry.FES.unit.solventcap array dbl
  -1.000000
  0.0
  0.0
  0.0
  0.0
!entry.FES.unit.velocities table dbl x dbl y dbl z
  0.0 0.0 0.0
  0.0 0.0 0.0
  0.0 0.0 0.0
  0.0 0.0 0.0
  0.0 0.0 0.0
  0.0 0.0 0.0
  0.0 0.0 0.0
  0.0 0.0 0.0
  0.0 0.0 0.0
  0.0 0.0 0.0
  0.0 0.0 0.0
  0.0 0.0 0.0
  0.0 0.0 0.0
  0.0 0.0 0.0
  0.0 0.0 0.0
  0.0 0.0 0.0

Now I have created topology and coordinates files successfully, and
xleap write down a number of lines saying
building topology
building atom param
building angle param
building proper torsion params
1-4: angle 1 4 duplicates ('triangular' bond) or angle ('square' bond)
1-4: angle 1 2 duplicates ('triangular' bond) or angle ('square' bond)
    1-4: angle 2 3 ...
1-4: angle 2 4...
1-4: angle 3 4...
  1-4: angle 5 8 ...
1-4: angle 5 11...
1-4: angle 5 14...
1-4: angle 8 14...
1-4: angle 8 11..
1-4: angle 11 14 ...
building improper torsion param
total 0 improper torsion applied
building H-Bond param
not making pre-residue atom chain types
making per-residue atom chain types
(Residues lacking connect0/connect1-
these don't have chain types marked:

res total affected
FES 5
)
(no restraints)

This is the pdb file from the new parametrisation:
REMARK
ATOM 1 S1 FES 1 34.447 34.094 111.212
ATOM 2 S2 FES 1 33.848 33.897 114.767
ATOM 3 S3 FES 1 36.832 35.519 113.511
ATOM 4 S4 FES 1 36.543 31.924 113.185
ATOM 5 FE1 FES 2 34.634 35.304 113.224
ATOM 6 CB FES 2 31.984 37.285 113.115
ATOM 7 SG FES 2 33.787 37.364 113.280
TER
ATOM 8 FE2 FES 3 34.363 32.588 112.931
ATOM 9 CB FES 3 33.352 29.697 112.009
ATOM 10 SG FES 3 33.038 30.838 113.289
TER
ATOM 11 FE3 FES 4 36.083 33.652 114.690
ATOM 12 CB FES 4 38.546 32.478 116.891
ATOM 13 SG FES 4 36.839 33.007 116.844
TER
ATOM 14 FE4 FES 5 36.595 33.848 111.968
ATOM 15 CB FES 5 37.983 34.648 108.903
ATOM 16 SG FES 5 38.200 33.520 110.342
TER
END


Regards
Boutheina


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Received on Sun Nov 25 2007 - 06:07:10 PST
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