AMBER Archive (2008)

Subject: AMBER: umbrella sampling for proton transfer

From: cniu_at_ualberta.ca
Date: Tue Mar 25 2008 - 19:30:33 CDT

Hi, all,

As a new user for amber, I am trying to run some umbrella sampling to
study the catalytic reaction of an enzyme using AMBER9. The reaction
involves a proton being transferred from S-H of a cys to N of a His.
Following is the input file:

&cntrl
   imin = 0,
   ntx = 7, irest = 1,
   ntb = 2, pres0 =1.0, ntp = 1,
   taup = 2,
   ntr = 0,
   cut = 20,
   ntc = 2, ntf = 2,
   tempi = 300.0, temp0 = 300.0,
   ntt = 3,
   gamma_ln = 1.0,
   nstlim = 5000, dt = 0.001,
   ntpr = 1, ntwx = 500, ntwr = 1000,
   nmropt = 1
  /
  &wt type = 'DUMPFREQ', istep1 = 10 /
  &wt type = 'END' /
  DISANG = s_h_n.RST
  DUMPAVE = s_h_n_vs_t.1

and s_h_n.RST is
&rst iat = 2238,2239, r1=0.0, r2=1.5, r3=1.5, r4=90.0, rk2=50., rk3=50., /
&rst iat = 615,2239, r1=0.0, r2=2.5, r3=2.5 r4=99.0, rk2=50., rk3=50., /

and part of result of s_h_n_vs_t.1 is
        0 1.336 2.705
       10 1.336 2.486
       20 1.336 2.407
       30 1.336 2.567
       40 1.336 2.481
       50 1.336 2.413
       60 1.336 2.494

The hydrogen atom in question is initially bonded to S @ 1.3 ang, I
would like to simulate this proton leaving the sulfur atom and moving
closer to a nearby nitrogen (initially at 2.7 ang).

My questions are:
1. why the distance between S and H stays at the same value? I tried
to increase the value of rk2 and rk3 to something like 500, but S-H
still keeps at 1.336. I made a test run to increase the distance
between convalently bonded S and C, and the value of S-C distance did
change. So I guess there must be something special to deal with
hydrogen in Amber. Am I right? What should I do to deal with this
problem?
2. Am I right to use more than one restraints in s_h_n.RST to run
umbrella sampling (like reaction coordinate R=r1-r2)? In fact, my
"real" mechanism will likely involve more than 3 restraints.

Thanks in advance to anyone that will give any suggestion.

Amara

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu