[gmx-users] selecting res CYS from G53a5 using pdb2gmx

Justin Lemkul jalemkul at vt.edu
Mon Jan 7 02:54:15 CET 2013

On 1/6/13 4:45 PM, Payman Pirzadeh wrote:
> Hi,
> I am using gromacs 4.5.4, and I am generating a topology file using G53a5
> force field. My protein has a Cys residue which is supposed to be in
> thiolate state (negatively charged side chain). During issuing the pdb2gmx
> command I use the switch -inter to be prompted about the charge state of the
> ionisable side chains, but it asks nothing about Cys side chains except
> about they being involved in disulfide bonds. My questions are:
> 1. how can I get pdb2gmx ask me about the charge status of Cys residues? Or
> do I need to manually change their status in the topology file and output
> gro file (removing the HG)?
> 2. I checked the aminoacid.rtp of G53a5, and it seems that for CYS, the
> total charge of the residue does not add to -1 but -0.5. Is anyone aware of
> any modifications to this force field parameters?

I don't know of any.  The AMBER force fields have parameters for the thiolate 
form of cysteine, but I've never seen them for Gromos96 force fields.  That 
doesn't mean they don't exist, of course, but this is the sort of thing one 
should research prior to choosing a force field and then hoping for a solution 
later ;)



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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