> The point is exactly that I don't want to perform optimization, so I
> would not change the force field itself but I would just change the
> "initial" structure of my "protonated" protein according to a N-H
> distance I select.
For this you could build a new residue template with the desired
distance. Then if there is no H in the pdb, the template will be
applied on loadpdb to generate the H at the desired location.
There's a bit of learning curve on this.
> If I have understood correctly, the only way to do that is to accept
> the initial addition of H atoms and than optimize with restrains using
> modified parameters.
This might be easier.
> Just to let me know if I have understood correctly:
> when you say
> > However, changing that file WILL do what you want it to.
> do you mean that after processing (opt or MD) this system it will take
> into consideration the parameters I added in the frcmod but it will
> not change my initial structure according to this parameters?
*During* min or md the params would be used. Everything would be
subject to movement unless you use 'belly' on just the H, in which
case I think you'd get what you want.
Bill
> I know it is not suggested to modify these files and before to start
> to play with other libraries I just decided to disturb you all.
> Thank you very much for your help (both Jason and Bill)
> Best
> Ivan
> Def. Quota Jason Swails <jason.swails.gmail.com>:
> > 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.
> >>
> >>
> >>
> >> ----------------------------------------------------------------
> >> This message was sent using IMP, the Internet Messaging Program.
> >>
> >>
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Graduate Student
> > 352-392-4032
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> --
> --
> Ivan Rivalta, PhD
> Dipartimento di Chimica - Università della Calabria
> Via P. Bucci, Cubo 14/C Piano 7
> 87036 Arcavacata di Rende (CS)
> Italy
> Telefono +39-3293441520
> Fax +39-0984-49-3390
> E-mail: rivalta.unical.it
> ------
> current work address:
> ETH Zurich
> Computational Science
> Department of Chemistry and Applied Biosciences
> Via Giuseppe Buffi 13, USI-Campus
> 6900 Lugano (Switzerland)
> Phone: +41 58 666 48 05
> Fax: +41 58 666 48 17
> E-mail: ivan.rivalta.phys.chem.ethz.ch
> ----------------------------------------------------------------
> This message was sent using IMP, the Internet Messaging Program.
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Received on Tue May 25 2010 - 18:00:04 PDT
