AMBER Archive (2009)

Subject: Re: [AMBER] Input file of the second stage RESP fitting

From: Cen Gao (cengao_at_gmail.com)
Date: Tue Mar 17 2009 - 16:24:24 CDT

Dear Dr. Dupradeau:
Thanks so much for your insightful reply. This really clarifies a lot
of things that I have not been able to fully understand. Also thanks
again for making this R.E.D tool for us to use.

Regards,

Cen

On Tue, Mar 17, 2009 at 9:32 AM, FyD <fyd_at_q4md-forcefieldtools.org> wrote:
> Dear Cen,
>
> Long answer, sorry... Do not hesitate to ask if you have other questions.
> This is a quite complex topic, and the RESP program documentation is not
> anymore available in the last version of Amber.
>
>> Sorry to trouble, I have several questions regarding the input file of
>> the second stage RESP fitting. Any input is highly appreciated.
>
> You can find many examples of inputs for the RESP program in R.E.DD.B.:
> See for instance:
> - A basic project: a single molecule/single conformation/single orientation
> RESP charge derivation: project "W-1":
> http://q4md-forcefieldtools.org/RED/up/W-1/
> To get the RESP input(s) belonging to a R.E.DD.B. project, just download the
> corresponding .bz2 file, or get the input(s) using such links:
> 1st RESP stage of W-1 project:
> http://q4md-forcefieldtools.org/RED/up/W-1/input1.in
> 2nd RESP stage of W-1 project:
> http://q4md-forcefieldtools.org/RED/up/W-1/input2.in
>
> - More complex projects involving multiple molecules: project "W-46"
> http://q4md-forcefieldtools.org/RED/up/W-46/
> http://q4md-forcefieldtools.org/RED/up/W-46/input1.in
> http://q4md-forcefieldtools.org/RED/up/W-46/input2.in
>
> - 1st Remark: in the case of ESP charge derivation, you need a single RESP
> input, as in the project "W-48"
> http://q4md-forcefieldtools.org/RED/up/W-46/
> http://q4md-forcefieldtools.org/RED/up/W-46/input1.in
> This means input2.in does not exist in this case.
>
> - 2nd remark: R.E.D. generates input(s) for the RESP program which are
> commented. For instance for the W-1 project:
>
> A classical input for the RESP stage one would be (DMSO molecule):
> ---------------------------------------------
>  TITLE
>  &cntrl
>  ioutopt=1, iqopt=1, nmol=1, ihfree=1, irstrnt=1, qwt= 0.0005
>  &end
>  1.0
>  TITLE
>    0   10
>    6    0
>    1    0
>    1    0
>    1    0
>   16    0
>    8    0
>    6    0
>    1    0
>    1    0
>    1    0
>
>
> ---------------------------------------------
> R.E.D. generates such an input1 instead (with comments):
>
>  RESP-A1 project. RESP input generated by R.E.D.
>  &cntrl
>  ioutopt=1, iqopt=1, nmol=1, ihfree=1, irstrnt=1, qwt= 0.0005
>  &end
>  1.0
>  Dimethylsulfoxide
>    0   10          Column not used by RESP (Added by R.E.D. for information)
>    6    0                         1
>    1    0                         2
>    1    0                         3
>    1    0                         4
>   16    0                         5
>    8    0                         6
>    6    0                         7
>    1    0                         8
>    1    0                         9
>    1    0                        10
>
>
> ---------------------------------------------
> R.E.D. generates such an input2 (with comments):
>
> RESP-A1 project. RESP input generated by R.E.D.
>  &cntrl
>  ioutopt=1, iqopt=2, nmol=1, ihfree=1, irstrnt=1, qwt= 0.001
>  &end
>  1.0
>  Dimethylsulfoxide
>    0   10          Column not used by RESP (Added by R.E.D. for information)
>    6    0                         1
>    1    0                         2
>    1    2                         3
>    1    2                         4
>   16   -1                         5
>    8   -1                         6
>    6    1                         7
>    1    2                         8
>    1    2                         9
>    1    2                        10
>
>
> ---------------------------------------------
>
>> 1. How does the ivary variable assigned for each atom in the input
>> file of second stage RESP? (this value was suggested to set to 0 in
>> the first stage) R.E.D. tool seems to assign it depending on the P2N
>> file made by Ante_RED.pl.
>
> 0: is for charge values of atoms which are (re-)computed & not equivalenced
> (in the considered stage)
> X: charge value to be (re-)computed & equivalenced with the atom number X in
> the atom order
> -1 (or -99): charge value not recomputed (in the considered stage) but
> frozen
>
> Only the charges of CH2 & CH3 groups are recomputed/equivalenced in the 2nd
> RESP stage; all other groups (if equivalent or considered equivalent by the
> user) should be equivalenced in the 1st stage and the corresponding charge
> values frozen in the stage 2.
>
> Let's take two characteristic examples:
> -Ethanol:
>   1st input   2nd input
> 1 C    0            0
> 2 H    0            0
> 3 H    0            2   "2" means equivalent to H2 in stage 2
> 4 H    0            2
> 5 C    0            0
> 6 H    0            0
> 7 H    0            6   "6" means equivalent to H6 in stage 2
> 8 O    0           -1  "-1" (or "-99") means keep charge from stage 1
> 9 H    0           -1
>
> -Ethan-1,2-diol
>  1 O   0           -1
>  2 H   0           -1
>  3 C   0            0
>  4 H   0            0
>  5 H   0            4
>  6 C   0            3
>  7 H   0            4
>  8 H   0            4
>  9 O   1           -1  "1" means equivalent to O1 in stage 1
> 10 H   2           -1  "2" means equivalent to H2 in stage 1
>
>> On the other hand, respgen in $AMBERHOME/bin
>> can also automatically generate input from an .ac file. I was
>> wondering if I should preferably use one over the other?
>
> For R.E.D. tools:
> See http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#3
> and Sections:
>  "General information about charge fitting"
>  "Rules followed by the R.E.D. program for automatic RESP input generation"
>
> Yes, the idea behind Ante_RED & the P2N file format is to rigorously limit
> the number of constraints used during the RESP or ESP fit to lead to low
> RRMS values (using a semi-automatic approach) - not only in basic single
> molecule charge derivation, but also in complex multiple molecule charge
> derivation involving specific charge constraints (such as intra-molecar
> charge constraint, inter-molecar charge constraint and inter-molecar charge
> equivalencing).
>
> Antechamber generates RESP inputs only for simple case involving single
> molecule approach/organic molecule cases. This 'totally automatic' procedure
> to generate the RESP input is particularly efficient in these simple cases.
> In these basic cases, Ante_R.E.D. and Antechamber should generate the same
> RESP input (if you master the P2N file correction).
>
> Now in more complex cases (R.E.D. has been designed for these complex cases)
> I do not think the automatic approach of Antechamber can be used (in all the
> cases you cannot check it as not yet available), and I do think the
> semi-automatic approach implemented in Ante_R.E.D./R.E.D. is the correct one
> (if you are interested in generating RESP inputs with a minimum number of
> charge constaints).
>
>> We already
>> have the electric potential generated on a grid so we only need the
>> input file to do resp. Can I easily get the input without running the
>> QM calculations if R.E.D is used? (We only do single conformation
>> charge fitting)
>
> You can indeed generate those inputs by hands and run RESP manually;
> However, after, you will have to add the derived charge values (by hand as
> well) in the force field library. Thus, if you have the MEP, this means you
> have the optimized structure. Right ? Why not running R.E.D. from the
> optimized structure (or Antechamber from the MEP) ? You should see which
> RESP input(s) would be expected. You can send me the PDB file of your
> structure and I can check the corresponding P2N file for you if you wish. We
> will propose this service in R.E.D. Server.
>
> See many examples of P2N file @
> http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php
>
>> 2. I suppose "-1" and "-99" means the same in the ivary section,
>> right? (charge frozen at initial charge?)
>
> Yes
>
>> 3. What does the "-99 29" mean in line 7 of the bis_1.in file at
>> $AMBERHOME/examples/resp_charge_fit/bis-napthyl/bis_1.in. From the
>> manual, this line refers to "charge, iuniq"? I don't get the charge
>> part. -99 certainly cannot be the net charge of that molecule. Does
>> the "-99" mean the same as the one in ivary, which indicates "charge
>> frozen at initial charge"? But there is no initial charge file
>> available (-q option was not supplied in this stage).
>
> I agree with you. If you look at the RESP output, you will get a
> confirmation of what you said:
>  Total charge (ich):-99
>  Number of centers: 29
>
> Moreover, if you look at the total charge:
>  Sum over the calculated charges:     -1.995
>
> This is not an integer. This case seems quite specific. Just forget it ;-)
> Use examples from somewhere else.
>
> regards, Francois
>
>
>
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