Re: AMBER: modifications to force field for Fe4S4 cubane

From: Bouthe´na Kerkeni <b.kerkeni.ucl.ac.uk>
Date: Wed, 28 Nov 2007 21:31:02 +0000

I still cannot obtain my prmtop and inpcrd files for the cubane and

XLEAP MESSAGE IS:

FATAL: Atom .R<CY 2>.A<O1 4> does not have a type.
FATAL: Atom .R<CY 2>.A<CB1 5> does not have a type.
FATAL: Atom .R<CY 2>.A<SG1 6> does not have a type.
FATAL: Atom .R<CY 2>.A<N2 7> does not have a type.
FATAL: Atom .R<CY 2>.A<CA2 8> does not have a type.
FATAL: Atom .R<CY 2>.A<C2 9> does not have a type.
FATAL: Atom .R<CY 2>.A<O2 10> does not have a type.
FATAL: Atom .R<CY 2>.A<CB2 11> does not have a type.
FATAL: Atom .R<CY 2>.A<SG2 12> does not have a type.
FATAL: Atom .R<CY 2>.A<N3 13> does not have a type.
FATAL: Atom .R<CY 2>.A<CA3 14> does not have a type.
FATAL: Atom .R<CY 2>.A<C3 15> does not have a type.
FATAL: Atom .R<CY 2>.A<O3 16> does not have a type.
FATAL: Atom .R<CY 2>.A<CB3 17> does not have a type.
FATAL: Atom .R<CY 2>.A<SG3 18> does not have a type.
FATAL: Atom .R<CY 2>.A<N4 19> does not have a type.
FATAL: Atom .R<CY 2>.A<CA4 20> does not have a type.
FATAL: Atom .R<CY 2>.A<C4 21> does not have a type.
FATAL: Atom .R<CY 2>.A<O4 22> does not have a type.
FATAL: Atom .R<CY 2>.A<CB4 23> does not have a type.
FATAL: Atom .R<CY 2>.A<SG4 24> does not have a type.
Failed to generate parameters
Parameter file was not saved.


WHAT I DID:

I have created a pdb file for Fe4S4: fes.pdb, and another for the 4
cysteines altogether cyf.pdb
in the latter I had to change the name of the SG,CB,CA,N,C,O to
SG1,CB1,CA1,N1,C1,O1
...
SG4,CB4,CA4,N4,C4,O4

Because all belong to the same residue and cannot have same name.
I have created a frcmod file for this.
when I use xleap:
loadoff fes.lib
loadoff cyf.lib
loadamberparams fe4s4cyf.frcmod
2FRV=loadpdb 2FRV-cut.pdb
xleap says: total atoms in file:32
the file contained 24 atoms not in residue templates (I guess thesse
are the SG1....O4 atoms)
bond 2FRV.1.FE1 2FRV 2.SG1
...
bond 2FRV.1.FE4 2FRV 2.SG4
check CYF
Unit is OK
check FES
unit is OK
check 2FRV
FATAL: Atomxxx <N1 1> does not have a type
...
FATAL: Atomxxx <SG4 24> does not have a type
an't find angle parameter: S2 - FE -
Could not find angle parameter: S2 - FE -
Can't find angle parameter: S2 - FE -
Could not find angle parameter: S2 - FE -
Can't find angle parameter: S2 - FE -
Could not find angle parameter: S2 - FE -
Can't find angle parameter: S2 - FE -
Could not find angle parameter: S2 - FE -
Can't find angle parameter: S2 - FE -
Could not find angle parameter: S2 - FE -
Can't find angle parameter: S2 - FE -
Could not find angle parameter: S2 - FE -
Can't find angle parameter: S2 - FE -
Could not find angle parameter: S2 - FE -
Can't find angle parameter: S2 - FE -
Could not find angle parameter: S2 - FE -
Can't find angle parameter: S2 - FE -
Could not find angle parameter: S2 - FE -
Can't find angle parameter: S2 - FE -
Could not find angle parameter: S2 - FE -
Can't find angle parameter: S2 - FE -
There are missing parameters.
check: Errors: 24 Warnings: 8


Can any one help me with this?
Thanks in advance
regards
Boutheina

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Received on Sun Dec 02 2007 - 06:07:13 PST
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