[gmx-users] Re: Problems about the simulation involving cytochrome C

[Mark Abraham]

On 13/04/2011 3:56 PM, Hui Sun wrote:
> Dear sir,
> I am very sorry to trouble you!

Unfortunately I am not able to act as a private tutor. Please direct 
such inquiries to the GROMACS mailing list.

> Now I want to do some work about Cytochrome C using Gromos force 
> field, but I don't know how to make some modifications for the force 
> field to introduce chemical connectivities that are specific to this 
> protein, viz., the bonds from Cys 14 and Cys 17 to the porphyrin ring 
> and to hold the ligands (Met 80 and His 18) bound to the heme 
> iron. See your message in the gmx-users mailling lists about the 
> similar problem! 
> (http://lists.gromacs.org/pipermail/gmx-users/2008-January/032039.html) I 
> wonder if the problem has been solved? Could you give me more details 
> about the missing parameters, such as bonds, angles and the 
> corresponding force constants for bonds, angles and dihedral angles?

No. That is either months of hard work for an expert, or hours of 
literature searching if someone's already done it for a similar system. 
Please read the link I gave in that post.

Mark