[gmx-users] Problem with FE-Cys covalent bond

Suman Nandy nandy.suman at rediffmail.com
Wed Jan 11 09:14:40 CET 2012

Dear gromacs users,

I have a problem regarding the simulation of Fe4S4 cluster attached to CYS of a protein using opls ff. I editted the "aminoacids.rtp" file as like this.

[ SF4 ]
... [ atoms ]
FE1 opls_966 2.500 1
FE2 opls_967 2.500 1
FE3 opls_968 2.500 1
FE4 opls_969 2.500 1
S1 opls_970 -2.000 1
S2 opls_971 -2.000 1
S3 opls_972 -2.000 1
S4 opls_973 -2.000 1
[ bonds ]
FE1 S1
FE1 S2
FE1 S3
FE2 S1
FE2 S2
FE2 S4
FE3 S2
FE3 S3
FE3 S4
FE4 S1
FE4 S2
FE4 S3

and also "atomtypes.atp" as

opls_966 55.84500 ; FE1: HEME
opls_967 55.84500 ; FE2: HEME
opls_968 55.84500 ; FE3: HEME
opls_969 55.84500 ; FE4: HEME
opls_970 32.06000 ; S1: S
opls_971 32.06000 ; S2: S
opls_972 32.06000 ; S3: S
opls_973 32.06000 ; S4: S

I have also added a line to "specbond.dat" regarding the SG-FE covalent bond. But while running the pdb2gmx command, (withouit any error) it just adds a H with SG (where the FE to bind)and there is no information on SG-FE bond in topology file. Please help.

Suman Kumar Nandy
Senior Research Fellow
Department of Biochemistry & Biophysics
University of Kalyani
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