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
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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