[gmx-users] Re: Problems with CYS in FeS4 clusters

David van der Spoel spoel at xray.bmc.uu.se
Tue Dec 10 11:36:48 CET 2002

On Tue, 2002-12-10 at 10:58, Ernesto E. Di Iorio wrote:
> Hi there!
> Last week I sent an email to all gromacs users to find out how to treat an 
> FeS4 cluster. You kindly and promptly answered my email with instructions 
> on how to solve the problem. Accordingly, I have modified the ffG431a*itp 
> files to include the new bond, angle and dihedral types as well as the 
> proper charges for the CB and SG atoms of CYS1. Furthermore, I modifid the 
> specbond.dat file including a line like this
> CYS     SG      1       FE      FE      4       0.228   CYS1    FE
> When I try to generate a topology and the coordinates in gromacs format 
> under these conditions the four CYS residues involved in the formation of 
> the FeS4 cluster are missing the H atom attached to the backbone N. I have 
> tried to define a new type of CYS and also made an attempt using unmodified 
> ffG431a*itp files, but all I could generate is either fully protonated CYS 
> (namely with an H on both the N and the SG atoms) or CYS residues without 
> any H (neither on N nor on SG). Of course I can make the topology by hand 
You probably need another CYS type than CYS1, use CYS2, that has no
hydrogen on SG and should work straight in pdb2gmx



More information about the gromacs.org_gmx-users mailing list