Hello!
I have a question about how to change the default values assigned to
bonds (and angles, dihedral angles, etc..) by tleap.
I would like to add H atoms to my xray pdb structure of a protein with
a bond distance chosen by me.
Since I want to use leaprc.ff99SB I was thinking that just changing
the equilibrium values of a given bond (i.e. backbone N-H, from 1.01
to 1.04) in the file:
/mydir/amberYY/dat/leap/parm/parm99.dat
would be enough.
However, it seems that it doesn't work and even if I use a modified
parm99.dat (which is the one loaded by tleap when I use source
laprc.ff99SB) my pdb output file of the protein still shows the
default (1.01 for H-N) bond distance value.
What I am missing?
Someone can help me?
Thank you so much in advance.
Note: just to be sure I am not making a mistake in the atom type I
have modified all the H*-N* bond distances.
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Received on Tue May 25 2010 - 16:30:04 PDT
