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

Hi: Did you add the parameters for the new covalent bond to the correct part of ffbonded.itp? Because, for the GROMOS FF you have to add the parameters for the new bond, angle and dihedral ,created due to specbond, in a certain part of the ffbonded.itp for pdb2gmx be able to use it. I dont know if

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

On 11/01/2012 7:14 PM, Suman Nandy wrote: 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

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

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 -2.00