Dear Amber users,
My structure consists of a core Fe-S cluster with fe linked to dendrimer
arms ( benzene rings with ether linkages and terminated with carboxyl
group).
I tried to generate the frcmod file using antechamber using parmchk :
parmchk -i file.mol2 -f mol2 -o frcmod
it gives me error as ATTN NEEDS REVISION.
I would like to have your suggestion regarding how should I generate the
frcmod file if I have my model in place of cysteine linkages with the
ferrous sulphide cluster .
In my model the sulphur in C-S-Fe link. My Carbon is a part of the benzene
ring. Can anybody suggest what modifications I should go for in my .frcmod
file or how should I generate my parameter file since antechamber does not
like it .
Below I have text of my leap log file and I have attached the library file
of my model.(I have used the frcmod.fe4s4 file from Dr. David Case group
where the sulphur was linked to CYS )
> gaff = loadamberparams gaff.dat
Loading parameters: /usr/local/apps/amber9/dat/leap/parm/gaff.dat
Reading title:
AMBER General Force Field for organic mol., add. info. at the end (June,
2003)
> loadoff d.off
Loading library: ./d.off
Loading: d
> edit d
> loadamberparams frcmod1
Loading parameters: ./frcmod1
Reading force field modification type file (frcmod)
Reading title:
remark goes here
> loadamberparams frcmod2
Loading parameters: ./frcmod2
Reading force field modification type file (frcmod)
Reading title:
remark goes here
> loadamberparams frcmod4
Loading parameters: ./frcmod4
Reading force field modification type file (frcmod)
Reading title:
remark goes here
(UNKNOWN ATOM TYPE: Fe)
> loadamberparams frcmod.fe4s4
Loading parameters: ./frcmod.fe4s4
Reading force field modification type file (frcmod)
Reading title:
parameters for Fe4S4S(CH3)4 2-
(UNKNOWN ATOM TYPE: SB)
(UNKNOWN ATOM TYPE: SM)
(UNKNOWN ATOM TYPE: FS)
> check d
Checking 'd'....
WARNING: There is a bond of 20.058054 angstroms between:
------- .R<T111 1>.A<S1 11> and .R<FS4 12>.A<FE1 1>
WARNING: There is a bond of 77.848345 angstroms between:
------- .R<FS4 12>.A<FE4 4> and .R<T111 35>.A<S1 11>
WARNING: There is a bond of 35.327556 angstroms between:
------- .R<FS4 12>.A<FE3 3> and .R<T111 24>.A<S1 11>
WARNING: There is a bond of 4.524847 angstroms between:
------- .R<T111 13>.A<C2 3> and .R<T111 13>.A<S1 11>
ERROR: The unperturbed charge of the unit: 0.250400 is not integral.
WARNING: The unperturbed charge of the unit: 0.250400 is not zero.
Checking parameters for unit 'd'.
Checking for bond parameters.
Could not find bond parameter for: sh - FS
Could not find bond parameter for: FS - sh
Could not find bond parameter for: FS - sh
Could not find bond parameter for: FS - sh
Checking for angle parameters.
Could not find angle parameter: sh - FS - SB
Could not find angle parameter: sh - FS - SB
Could not find angle parameter: sh - FS - SB
Could not find angle parameter: c - sh - FS
Could not find angle parameter: SB - FS - sh
Could not find angle parameter: SB - FS - sh
Could not find angle parameter: SB - FS - sh
Could not find angle parameter: SB - FS - sh
Could not find angle parameter: SB - FS - sh
Could not find angle parameter: SB - FS - sh
Could not find angle parameter: SB - FS - sh
Could not find angle parameter: SB - FS - sh
Could not find angle parameter: SB - FS - sh
Could not find angle parameter: FS - sh - c
Could not find angle parameter: FS - sh - c
Could not find angle parameter: FS - sh - c
There are missing parameters.
check: Errors: 1 Warnings: 5
Thanks and Regards
Kirtana
- application/octet-stream attachment: d.off
Received on Mon Jul 06 2009 - 12:14:15 PDT
