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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Jun 27 2010 - 20:30:03 PDT
