AMBER Archive (2009)

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

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Tue Mar 17 2009 - 08:32:58 CDT

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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