[gmx-users] Re: HEME connections

David spoel at xray.bmc.uu.se
Wed Jan 15 19:24:52 CET 2003

On Wed, 2003-01-15 at 19:50, muthu12 wrote:
> Dear david
> I want run cytochrome c simulation
> with two extra bonds for hem with two cys residues
> and another two extra bond for FE as shown in crystal 1HRC
> when I run pdb2gmx with -inter It provides me an option to add only
> one bond for each. HHow can I add aditional two bonds for the simulation.
> Is there any way to edit the topology file afterwards
> thank you
No you have to do it at the pdb2gmx stage.
pdb2gmx detects only one of the cys - CA* bonds, because the length is
not correct. It does find the His-Fe bond. The link to methionine is not
covalent, therefore no bond is made. You will have to check whether the
orientation is maintained properly, otherwise you could consider adding
a distance restraint between sulphur and FE,

You might want to tune the specbond.dat file to have the distance
between CAB and FE be 0.18 iso 0.2
> Prabhakaran
> long time GROMACS user and bought the commercial version
Which does not exit anymore, but thanks anyway. Would you be so kind as
to direct further questions to the gmx-users mailing list?
Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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