AMBER Archive (2008)

Subject: AMBER: Reg cysteine protonaitons states in pH constant MD

From: D.Usharani (
Date: Sun Jan 27 2008 - 23:15:58 CST

Dear Amber Users,

I would like to do pH constant MD with cysteine protonation states. I
didnt find these resdiue details in But in all_amino02.lib the
CYS and CYM are the protnated and deprotonated states of cysteine where
charges are given. To fill the complete details of unkown residue in, I need a relative energy of states. So I tried the the ADVANCED
tutorial A6
"pKa Calculations Using Thermodynamic Integration"

I followed the same procedure for cysteine like asp, but since I have
amber 8 I was unable to perform the calculation. It gives me pert. prmtop
file is needed. (I am running it in a LINUX PC)

command used is "sander -O -i -p cys.prmtop -c cys.inpcrd -o
cys_modelstep0.out -inf -x cys_modelstep0.mdcrd -r
cys_modelstep0.rst "

Could any one tell me what is that I additionally should provide if I have
to run in amber8.

Is there any reference that is there already known about the relative
energies of cysteine protonated states?

Thank you in advance

Best regards

c/o Prof E.D.Jemmis
Inorganic and PhysicalChemistry
Indian Institute of Science
Bangalore -560012

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