AMBER Archive (2007)

Subject: AMBER: Reproducing constant pH results !!

From: Pradipta Bandyopadhyay (pradipta_b_at_mail.jnu.ac.in)
Date: Thu Sep 27 2007 - 00:16:49 CDT

Dear All,

  I am trying to reproduce the results of constant pH simulation in the JCC paper (Mongan, Case, McCammon).
I am using AMBER 8. I tried the 1AKI structure of Lysozyme. I followed the protocol given in the paper (an input file is given later), except initial structure preparation by optimizing H-bond network was not done. All simulations were run for 1ns as done in the JCC paper.

The results I am getting is OK for some residues but very different for others. For instance, at pH=4 the pKas are

residue my result JCC paper (from Table 2)
ASP18 2.05 1.98
ASP48 0.93 1.94 ( I got only 8 MC transitions - perhaps this is one reason for this difference)
ASP87 1.98 3.12

One typical MD input file is like this

 md simulation
 &cntrl
 imin=0,irest=1,nstlim=100000,ntx=5
 ntpr=50,ntwr=100,ntwx=100,ntwv=100,
 ntt=1,temp0=300.0 tempi=300.0,tautp=2.0
 cut=30.0,scee=1.2,igb=2,saltcon=0.1,
 ntb=0,dt=0.002,nrespa=1,
 ntc=2,ntf=2,tol=0.000001
 icnstph=1,solvph=4.0,ntcnstph=5,
 &end

My questions are (a) What is causing this large difference for some residues - one is the initial structure is not prepared
                              using optimizing H-bond network? Anything else?
                         (b) Can anybody give me a structure of 1AKI where H-bond network is optimized?
                          (c) Is there anything wrong I am doing in MD (as seen from the input file).
                        
Any other help will be appreciated as well.

regards,

  Pradipta

Dr. Pradipta Bandyopadhyay
Associate Professor
Centre for computational biology and bioinformatics
School of Information Technology
Jawaharlal Nehru University, New Delhi, INDIA
http://www.jnu.ac.in/Faculty/pbandyopadhyay/

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