Hello,
Several comments regarding your email -- see below.
On Tue, May 25, 2010 at 7:14 PM, <rivalta.unical.it> wrote:
>
> 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
>
Do not do this. These files are meant to be untouched, and it would be
quite unfortunate if someone were to get these files from you (since you are
certainly allowed to redistribute as you will under the license).
parm99.dat will not be what they're expecting. You can use a force
modification file (frcmod) that has the parameters you wish to change. As
long as you load that file (loadamberparams frcmod), any parameters in that
file will overwrite the definitions that came before. (i.e., load the
frcmod AFTER you load ff99SB). These files are not intended to be changed.
However, changing that file WILL do what you want it to.
>
> 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.
>
This is because this has only affected the force field. The hydrogens are
added according to the template in the library file (OFF library, amber prep
file, or mol2 file). Thus, if the template has a N-H distance of 1.01, you
can change the equilibrium distance all you want, but it will never affect
the structure that leap gives you. However, as soon as you run any kind of
simulation (minimization or molecular dynamics) without SHAKE, the system
will naturally evolve to the equilibrium bond distance you set (if that is
what minimizes the entire energy).
A tip to get the bond distances where you want them: use ntr=1 and restrain
everything but the hydrogens (see restraintmask, and the syntax for amber
masks) with a very strong harmonic restraint. This will cause the hydrogen
bonds that you altered to relax to the new equilibrium position that you
specified.
Now, of course, I'm obliged to say that the equilibrium bond distances have
been well-parametrized, and such parameters as the backbone N-H distance
should probably only be messed with if you know what you're doing and
there's something specific you'd like to learn by doing so. However, that
being said, the instructions above should help get you where you claim to
want to go.
Good luck!
Jason
>
> 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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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Tue May 25 2010 - 17:00:03 PDT
