AMBER Archive (2009)
Subject: Re: [AMBER] non standart residue library creation with tleap (Zn atom)
From: Andrew Voronkov (drugdesign_at_yandex.ru)
Date: Tue Nov 24 2009 - 04:12:53 CST
Ok, the last question.
Accroding to linke given by you: "Having chosen or created one or more atom types and sets of van der Waals parameters, the bond, angle and dihedral parameters must be created. Equilibrium bond lengths and angles may be obtained from tabulations of experimental data in the literature. "
The X-ray crystallography is kind of experimental method which give equilibrium lengths and angles with some error which can be ok in case zinc atom is not so crucial.
Can you please say why I can't just measure bond lengths and dihedral angles parameters in the PDB structure which I want to use for MD. This will just fix the already existing parameters and that is what I need. Why I should gather or calculate prceise bond length and angle parameters if the PDB data already measured by X-ray analysis? The bond energies and VdW radii I can get from the papers, yes.
24.11.09, 10:26, "FyD" <fyd_at_q4md-forcefieldtools.org>:
> > Actually my situation is very similar to described in this tutorial:
> > http://www.rosswalker.co.uk/tutorials/amber_workshop/Tutorial_four/
> > there is no RESP calculations there. So points 1-2 are a bit
> > different there. Main point for me is the 3rd one.
> ok we finally progressed ;-)
> > Why can't I just take dihedral angles and bond length parameters
> > from the PDB file of the protein? It's the x-ray structure and zinc
> > is far from ligand's binding site so taking parameters directly
> > from PDB file can work then? I can actually try to use cap and not
> > include zinc at all, but I expect some conformational changes there
> > upon small ligand binding and second I just want to go through this
> > zinc parametrization:)
> So you need to manually create a frcmod file. You need to understand
> what information is available in a frcmod file.
> See http://ambermd.org/doc6/appendices.html
> > PS points 1-2 with usage of your server will also take significant
> > computational time as I understand.
> This is not only cpu time - this has to do with running jobs,
> analysing data, re-running jobs etc...
> Good luck.
> regards, Francois
> > 23.11.09, 20:50, "FyD" :
> >> Dear Andrew,
> >> Now, we know that you want to model a Zinc amino-acid complex with
> >> atom connectivities between this Zinc atom and the considered amino
> >> acids.
> >> Let's proceed by order: you could try the following plan:
> >> 1) First, do you have the charges of this complex ?
> >> if no, I suggest you to use R.E.D. and/or R.E.D. Server to derive RESP
> >> or ESP charges embedded in a force field library (.mol2 file). Here,
> >> you have to optimize and get the MEP by QM, and then fit the RESP or
> >> ESP charges to the MEP.
> >> See http://q4md-forcefieldtools.org/RED/
> >> & http://q4md-forcefieldtools.org/Tutorial/
> >> Three difficulties here:
> >> ? Define the atoms of this complex and the corresponding fragment to
> >> be inserted in your protein
> >> ? Select the right theoretical level for the QM steps
> >> ? the fitting step might fail
> >> => This step is time consuming and requires some experience (or you
> >> take Mulliken charges after charge equivalencing for chemically
> >> equivalent atoms).
> >> 2) Define the FF atom types for your complex:
> >> Using Cornell et al. J. Am. Chem. Soc. 1995, 117, 5179 - Table 1, add
> >> the FF atom types in the FF library obtained in step 1)
> >> For this step, use a LEaP script and the "set" command. See examples
> >> in R.E.DD.B. I already provided you.
> >> See http://q4md-forcefieldtools.org/REDDB/projects/W-46/
> >> http://q4md-forcefieldtools.org/REDDB/projects/W-46/script1.ff
> >> 3) Manually create the "frcmod" file for missing FF parameters:
> >> "source leaprc.ff99SB" & run LEaP without this "frcmod" file, try to
> >> save the prmtop/prmcrd files: LEaP will fail, but will report the
> >> missing FF parameters. You manually create your frcmod file using the
> >> listing of missing FF parameters reported by LEaP.
> >> => This step is time consuming and requires some experience in force
> >> field parameter development (and try to get FF parameters from
> >> literature).
> >> You have all to generate your prmtop/prmcrd files.
> >> I tried to make the plan as short as possible - steps 1-3 represent
> >> loooot of work.
> >> regards, Francois
> >> Quoting Andrew Voronkov :
> >> > How to create frcomd file then? Manually?
> >> >
> >> http://www.rosswalker.co.uk/tutorials/amber_workshop/Tutorial_four/section4.htm
> >> > - how was this frcmod file created? Where should I get bond and
> >> > dihedrals parameters then, to measure them in the protein or to make
> >> > estimation by some software?
> >> > I don't quite understand how Ross Walker has made that frcmod file.
> >> >
> >> > 23.11.09, 18:31, "FyD" :
> >> >
> >> >> Quoting Andrew Voronkov :
> >> >>
> >> >> > This is kind of zinc finger and it is connected to four amino acids,
> >> >> > not small molecule ligands. So in case of amino acids I should also
> >> >> > define frcmod for this zinc atom and four amino acids which are
> >> >> > bound to it? To construct frcmod file by antechamber or use the
> >> >> > frcmod file which I've mentioned above?
> >> >> > And the library in this case (saveoff zinc.lib) should also be
> >> >> > defined for the zinc atoms and four amino acids to which it is
> >> >> > connected, right?
> >> >>
> >> >> If you want to consider the whole complex i.e. Zinc-connected to
> >> >> amino-acids, you canNOT use what is available @
> >> >> http://q4md-forcefieldtools.org/Help/Andrew/
> >> >>
> >> >> You need to create a frcmod file + an off FF library for your Zn-amino
> >> >> acid complex.
> >> >>
> >> >> my mistake:
> >> >> I do NOT think Antechamber handles metal atoms.
> >> >>
> >> >> regards, Francois
> AMBER mailing list
AMBER mailing list