Subject: Re: [gmx-users] simulating Ubiquitinated protein

Mark Abraham Mark.Abraham at
Fri Jun 13 03:21:51 CEST 2008

> Thanks David, I could edit the specbond.dat and thus pdb2gmx could make the bond between the desired residues. However, still there are two problems..
> 1) Once the bond is formed the C-terminal glycine cannot be defined as a terminal one, but pdb2gmx treats it as a terminal residue and thus modifies it to put two oxygens.. Gly-COO- (but this can be taken care of by using -ter card while running pdb2gmx)
> However the second one is more problematic..i.e. addition of hydrogen to the modified Lysine residue. I cannot define it to put it in the same plane as NZ, CE and the C from Glycine. Is there anyway to do that?

As a general point, the people you're asking for help won't remember 
anything about where the modified lysine is in your sequence or how it 
has been modified. Do spell things out thoroughly.

Adding hydrogens is controlled by the hydrogen database files (.hdb 
files) whose format is described in Chapter 5 of the manual. It's 
possible you will be able to specify the C atom of a previous/subsequent 
residue with "-C" or "+C" respectively, in an entry for your modified 
lysine. Otherwise, you can either build it in by hand and let the energy 
minimization move it to the right location, or temporarily define a new 
"combined" gly-modlys residue that will let you make a new .hdb entry 
such that the new hydrogen can be specified with a intra-residue name.


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