AMBER Archive (2009)

Subject: Re: [AMBER] non standart residue library creation with tleap (Zn atom)

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Tue Nov 24 2009 - 03:26:37 CST

Andrew,

> 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

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