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 <drugdesign.yandex.ru>:
> 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" <fyd.q4md-forcefieldtools.org>:
>
>> 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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Received on Mon Nov 23 2009 - 12:00:02 PST
