Thank you very much Jason.
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.
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.
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?
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.
>>
>>
>>
>> ----------------------------------------------------------------
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>>
>>
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>>
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
> _______________________________________________
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> 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
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Received on Tue May 25 2010 - 18:00:03 PDT
