Dear Amir,
> I'm trying to generate input files (prmtop and inpcrd) of a protein that is
> bound in its N-terminal to a Myristoyl group which is essentialy a 14
> carbon fatty acid chain.
>
> I followed all steps to define the Myristoyl group (MYR) in xleap, which
> included adding charges, atom types and defining bonds.
> it seems ok up to this point..
So the total charge of the MYR fragment (below) should equal zero.
O
CH3(CH2)12C
In LEaP, the total charge of an unit can be easy checked by using:
charge MYR
If not, you could try using R.E.D. or R.E.D. Server at:
http://q4md-forcefieldtools.org
> Then, I loaded into xleap a PDB file that contains the Myristoyl group as
> the first residue (MYR), added bond between the first carbon of the Myr to
> the N atom of the first Residue in the protein.
If you correctly define the "tail" for the MYR fragment/force field
library you should not need to create this bond...
See
http://q4md-forcefieldtools.org/Tutorial/leap-mol3.php
> I saved the pdb and it seems that the bond was created (I can see it in
> pymol)
I do not think that displaying a structure to the PDB file format is a
graphical program is _the_ good way to check if a bond between two
atoms is indeed created or not. Indeed the graphical program will
automatically create a bond if the distance between the two atoms
involved is lower than an internally defined threshold.
On the contrary, you need to check that the _topology_ defined IN your
_force field library_ does take into account of this bond whatever is
the distance between the two atoms involved.
A good way to check that a bond in created between two key residues is
to display the prmtop/prmcrd file (without solvent) in VMD, or to look
at this bond in the LEaP program. But once again, if you correctly
define the "tail" in LEaP for the MYR fragment/force field library you
should not need to create this bond...
> However, when trying to generate *.prmtop and *inpcrd files I get the
> following message:
>
> *Could not find angle parameters: O2-C-N*
Did you define the "O2" atom types for the oxygen atom in a peptide bond?
It should be "O"...
> and the files failed to be saved
>
> I browsed the mailing lists and tutorial quit extensively, and I tried a
> *.frcmod file can fix that problem:
[...]
> ANGLE
> O -C -N 50.000 121.000 # calculated from the pdb 1HCD_MYR_tit.prmtop
[...]
-> parm99.dat; it is there (see N -C - O)...
> and when load it to xleap I get an error massage: *Unknown
> keyword:
>
> in parameter file*
>
> my questions are:
> 1) where is the mistake in my *frcmod file?
> 2) can these errors be bypassed somehow with incorporation of some default
> values?
> 3) Is generating a *.prepin file with antechamber and then creating a
> frcmod file the correct way?
You have an inconsistency between the "O" atom type defined in the
frcmod file and the "O2" atom type defined in your force field library.
In your case, not frcmod file should be required...
The mol2 file format is a force field library file format as the 'old'
prep one. However, it can be displayed in many graphical programs,
while the prep one cannot not. I would use the mol2 file format (or
mol3 file format) instead of the prep file format.
See
http://q4md-forcefieldtools.org/Tutorial/leap-mol2.php
vs
http://q4md-forcefieldtools.org/Tutorial/leap-mol3.php
to look at the advantages/disadvantages of the off, prep, mol2 & mol3
file formats...
regards, Francois
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Received on Wed Jan 25 2012 - 00:00:03 PST
