AMBER Archive (2003)

Subject: How do NTC=2 recognize hydrogen atom?

From: yuan bo (yuanbous_at_yahoo.com)
Date: Wed Feb 19 2003 - 04:24:55 CST

Dear Amber user
 Thanks for everyone who ever helped me, especially
for Mr David A.case.
  It is know that NTC=2 constrain bonds containing
hydrogen in MD simulation. I have one problem: How do
Amber recognize the hydrogen atom in MD simulation, by
atom type name( i.e the first letter in type name is
"H" ) or other characters?
  Because I have one idea, but I don't know if it is
right. If I do MD for two molecules(as solute) in
aqueous solution. I want to constrain bond containing
hydrogen for one solute molecule and all waters, at
the same time, constrain all bonds for the other
solute molecule represented by X-Y-Z three united
atoms model). I define X to be one new atom type whose
name begin with "H",i.e HX1 and Z atom is changed to
HX2 type. In MD simulation, if I set NTC and NTF=2, I
could constrain all bond length of the X-Y-Z solute
molecule and water bond length and not for the other
solute molecule.
  Is the method right? Could I come true my idea by
means of the method? Were HX1 and HX2 type used for
other H atom in Amber parameter file ( I use Amber 6).
Because I don't know how many and What atom name
begining with "H" were used for H atom? In other
words,How many and what atom and type name begining
with "H" are not applyed for H atom in Amber6
parameter file?
  Could Anybody give me some suggestions to help me
realize the idea? Any suggestion is deeply
appreciated.
yb

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