Dear Francois,
Thank you for your kind help! You are such a nice and patient person:)
I will try to follow your tutorial step by step. If I meet some other
problems, I will let you know.
Once again, thank you so much!
With my very best wishes,
Sincerely,
Jia
On Wed, Jun 30, 2010 at 2:07 PM, FyD <fyd.q4md-forcefieldtools.org> wrote:
> Dear Jia,
>
> Sorry for the delay... Yes, using the last version of the R.E.D. Tools is
> better. Once the R.E.D. Tools III.4 will be available you will have to apply
> the same corrections as these below.
>
> -I- Modifications of Ante_R.E.D. from the III.3 distribution
> Yes you need to add "AU" (capital letters) in An_R.E.D. as you started
> below
>
> *1* line 23 add in %Elements (authorize Gold to be used & provide its
> atomic number)
> ,AU =>"79" just after BR =>"35"
>
> *2* line 26 add in %Valence (define the maximum valency for Gold: useful
> for the topology of the FF library: the MOL2 file format generated at the
> end by R.E.D.)
> ,AU =>"4" (or Au =>"6", I do not know) just after BR =>"1"
>
> *3* line 26 add in %Radius (it is useful for the definition of the atom
> connectivities - it is different from the radius used in MEP computation!!!)
> ,AU =>"1.4" (1.5 should be OK; adapt if not) just after BR =>"1.210"
>
> => this will generate a P2N file & inputs for geometry optimization using
> Firefly, GAMESS-US and Gaussian.
>
> -1- check chemical equivalencing in the P2N file (in the first column of
> atom names)
> see http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#ATOM-NAME
> (Ante_R.E.D. 2.0 solves all here).
>
> -2- check the atom connectivity for Gold in the P2N file: you should have 4
> connections with Gold in your bio-inorganic complex (affected by the radius
> defined in *3* above: if not correct increase 1.5 to 1.6 etc...)
> see http://www.wwpdb.org/documentation/format30/index.html
>
> -3- check the total charge & spin multiplicity of your complex in the P2N
> file & QM inputs
>
> -4- adapt the QM input you use (GAMESS, Firefly or Gaussian) so that you
> select the theory level of your choice; as a starting point I would use
> B3LYP/6-31G* & you have to define an Effective Core Potential (ECP) for Gold
> (I think).
> => run the geometry optimization output without R.E.D. first to see how it
> goes with ECP...
>
> I would start using a small model such as [AuH4]+/-x before to switch on
> your bio-inorganic complex (quite big) to set up all the charge derivation
> process. This will allow you to quickly get results.
>
> =======
>
> -II- Modifications of R.E.D.-III.3
>
> *1* line 3872 add in %Elements (authorize Gold to be used & provide its
> atomic number)
> ,'AU' =>"79" just after 'BR' =>"35"
>
> *2* in the function "Readpdb"
> line 656 just before %L4atoms, add the following new code Line:
> %atomAU = ('AU'=>"79"); # Gold
>
> *3* in the function "Readpdb"
> line 658 add in "Twoletterelt"
> ,'AU' =>"AU" just after 'BR'=>"BR"
>
> *4* just before the ending bracket "}" line 870 of the function "Readpdb",
> add
> $TestAU[$NM]=0;
> for ($i=0; $i<$nbatoms[$NM]; $i++){
> if(exists $atomAU{$tab[1][$i][$NM]}){ $TestAU[$NM]=1; last; }
> }
>
> => Here, you create a variable $TestLAU[$NM] for each molecule (you will be
> able to derive charge for different Au complexes if you need); this variable
> = 1 if the Gold element is found in the P2N file.
>
> *5* line 1206-1230 you will find the lines to modify the geometry
> optimization input ("file handle JOB1_FILE"). With the variable you defined
> in *4* you can now modify the input according to the presence of the Gold
> element
> if ($TestAU[$NM]==1)) { print JOB1_FILE " blabla for GAMESS/Firefly \n"; }
>
> same idea with Gaussian input line 1306
> if ($TestAU[$NM]==1)) { print JOB1_FILE " blabla for Gaussian... \n"; }
>
> *6* line 1757-1793 you will find the lines to modify the MEP computation
> input ("file handle JOB2_FILE"). With the variable you defined in *4* you
> can again modify the input according to the presence of the Gold element
> if ($TestAU[$NM]==1)) { print JOB2_FILE " blabla for GAMESS/Firefly \n"; }
>
> Same idea with Gaussian input line 1874
> if ($TestAU[$NM]==1)) { print JOB2_FILE " blabla for Gaussian \n"; }
>
> *7* You need to find out about the radius of Gold to be used in MEP
> computation. For GAMESS/Firefly it is hard coded in the source code.
> For Gaussian, you need to provide it at the end of the input (after having
> jumped a line): See 1905-1911 (this part has been re-written is III.4)
> I would start with the 1.8 value & see how this cuisine works first ;-)
> Then you might decide to fine tune this value...
>
> This should be OK. It is not that difficult; you only need to proceed step
> by step starting from a basic Gold model and understand what you do. Then,
> when you will switch to your bio-inorganic complex you will only have to
> handle additional intra-molecular charge constraints for the two dipeptides
> involved in the charge derivation.
>
> Fore sure, here, a tutorial should be written... I hope this helps.
>
> regards, Francois
>
>
>
>
> Dear Francois,
>>
>> I really appreciate your kind help!
>>
>> If possible, would you please to tell me how to modify the source
>> code according to step 1 to step 3?
>>
>> On Fri, Jun 25, 2010 at 1:25 PM, FyD <fyd.q4md-forcefieldtools.org>
>> wrote:
>>
>> Dear Jia,
>>>
>>> I am trying to simulate a peptide with a metal-containing complex. As
>>>
>>>> shown in the attached picture, the gold atom (yellow ball) of
>>>> phenanthroline-gold is bound to N and S atoms of HIS and CYS,
>>>> respectively.
>>>> I used to calculate the resp charge of non-standard residue by R. E. D.
>>>> III.
>>>> It works fine. But I have no experience to work on small molecules.
>>>>
>>>> I would like to know if it possible to obtain the RESP charge of such a
>>>> heavy-metal contained complex which is bound to two residues?
>>>>
>>>>
>>> You need to solve several problems in R.E.D.-III.x to get charges for
>>> your
>>> Gold complex:
>>>
>>> 1) Add the "Au" atom in the source codes to authorize R.E.D. &
>>> Ante_R.E.D.
>>> to use "Au"
>>> 2) Add which "radius" value you want to use for "Au"
>>>
>>>
>> I have checked the perl scripts and found lines as follows. I guess the
>> type and radius of atom should be added in these lines, is it right?
>> However
>> I am not sure which one of the three kinds of radii(# Radii used by
>> Ante_R.E.D.; # Empirical radii; # Calculed radii ) is default, would you
>> please to tell me?
>>
>> # Information:
>> # One can modify the "$sort" & "$notlig" variables in the main section of
>> the program (line 591)
>> #
>> ######## Chemical elements recognized by Ante_R.E.D.: up to Bromine (Z =
>> 35)...
>> # 'Terminal' chemical elements that may generate vdW bumps in a bad
>> initial
>> structure
>> my %Terminal = (H =>"1",F =>"9",CL =>"17",BR =>"35");
>>
>> # Elements: Warning: Calcium is XX !!!
>> my %Elements = (H =>"1",LI =>"3",BE =>"4",B =>"5",C =>"6",N =>"7",O
>> =>"8",F
>> =>"9",NA =>"11",MG =>"12",AL =>"13",SI =>"14",P =>"15",S =>"16",CL
>> =>"17",K
>> =>"19",XX =>"20",SC=>"21",TI => "22",V=>"23",CR =>"24",MN=>"25",FE
>> =>"26",CO
>> =>"27",NI =>"28",CU =>"29",ZN =>"30",GA =>"31","GE" =>"32",AS =>"33",SE
>> =>"34",BR =>"35");
>>
>> # Maximal number of bonds for each chemical element
>> my %Valence = (H =>"1",LI =>"1",BE =>"2",B =>"3",C =>"4",N =>"4",O =>"2",F
>> =>"1",NA =>"1",MG =>"2",AL =>"6",SI =>"6",P =>"5",S =>"6",CL =>"1",K
>> =>"1",XX =>"2",SC=>"6",TI => "6",V=>"6",CR =>"6",MN=>"8",FE =>"6",CO
>> =>"6",NI =>"6",CU =>"6",ZN =>"6",GA =>"3","GE" =>"4",AS =>"3",SE =>"2",BR
>> =>"1");
>>
>> # Radii used by Ante_R.E.D.
>> my %Radius = (H =>"0.230",LI =>"0.680",BE =>"0.350",B =>"0.830",C
>> =>"0.680",N =>"0.680",O =>"0.680",F =>"0.640",NA =>"0.970",MG =>"1.100",AL
>> =>"1.350",SI =>"1.200",P =>"0.750",S =>"1.020",CL =>"0.990",K =>"1.330",CA
>> =>"0.990",SC=>"1.440",TI => "1.470",V=>"1.330",CR =>"1.350",MN=>"1.350",FE
>> =>"1.340",CO =>"1.330",NI =>"1.500",CU =>"1.520",ZN =>"1.450",GA
>> =>"1.220","GE" =>"1.170",AS =>"1.210",SE =>"1.220",BR =>"1.210");
>>
>> # Empirical radii: You might try the "Empirical radii" instead of the
>> "Radii
>> used by Ante_R.E.D."...
>> #my %Radius = (H =>"0.250",LI =>"1.450",BE =>"1.050",B =>"0.850",C
>> =>"0.700",N =>"0.650",O =>"0.600",F =>"0.500",NA =>"1.800",MG =>"1.500",AL
>> =>"1.250",SI =>"1.100",P =>"1.000",S =>"1.000",CL =>"1.000",K =>"2.200",CA
>> =>"1.800",SC=>"1.600",TI => "1.400",V=>"1.350",CR =>"1.400",MN=>"1.400",FE
>> =>"1.400",CO =>"1.350",NI =>"1.350",CU =>"1.350",ZN =>"1.350",GA
>> =>"1.300","GE" =>"1.250",AS =>"1.150",SE =>"1.150",BR =>"1.150");
>>
>> # Calculed radii: You might try the "Calculated radii" instead of the
>> "Radii
>> used by Ante_R.E.D."...
>> # my %Radius = (H =>"0.530",LI =>"1.670",BE =>"1.120",B =>"0.870",C
>> =>"0.670",N =>"0.560",O =>"0.480",F =>"0.420",NA =>"1.900",MG =>"1.450",AL
>> =>"1.180",SI =>"1.110",P =>"0.980",S =>"0.880",CL =>"0.790",K =>"2.430",CA
>> =>"1.940",SC=>"1.840",TI => "1.760",V=>"1.710",CR =>"1.660",MN=>"1.610",FE
>> =>"1.560",CO =>"1.520",NI =>"1.490",CU =>"1.450",ZN =>"1.420",GA
>> =>"1.360","GE" =>"1.250",AS =>"1.140",SE =>"1.030",BR =>"0.94");
>>
>>
>>
>> 3) Add which "theory level" you want to use during the geometry
>>> optimization & MEP computation step
>>>
>>>
>> I have little knowledge about quantum chemistry software such as
>> GUASSIAN and GAMESS, possibly as a result I failed to find the "theory
>> level" in the pl scripts. Would you please to help me?
>>
>>
>> 4) Select a target complex to be involved in charge derivation using the
>>> RESP program. Here, you need to imagine how you could include your
>>> complex
>>> in your whole molecule. You select a model & you use constraint(s) during
>>> the RESP fit to make your model compatible with the whole system: Once
>>> you
>>> understood the use of intra-molecular charge constraint in dipeptide for
>>> instance you can easily apply the same strategy to your Au complex (using
>>> two amino acid central fragment).
>>> See http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#10
>>>
>>> I can help you setting these steps if you need...
>>>
>>> The next version of the R.E.D. Tools source code is going to be
>>> distributed
>>> under the GNU General Public License. We will see if we can release III.4
>>> next week.
>>>
>>> I am now using R.E.D-III.2&GAMESS-US, is it better to wait for the
>>>
>> upcoming III.4 version?
>>
>>
>> regards, Francois
>>>
>>>
>>> Thank you so much!
>>
>> Best regards,
>> Sincerely,
>> Jia
>>
>
>
>
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Received on Wed Jun 30 2010 - 09:00:03 PDT
