Mod:Hunt Research Group/Jan resp

restrained charges and antechamber data

introduction

• see the installation pages for how to install antechamber
• more information on antechamber can be found here "http://ambermd.org/antechamber/ac.html"
• from the web-site above "Antechamber is a set of auxiliary programs for molecular mechanic (MM) studies. This software package is devoted to solve the following problems during the MM calculations: (1) recognizing the atom type; (2) recognizing bond type; (2) judging the atomic equivalence; (3) generating residue topology file; (4) finding missing force field parameters and supplying reasonable and similar substitutes."

basic input

• Like many scripts resp works by giving flags and arguments.
• flags and arguments relevant to us are:

-i filename.log gives the input file,

-fi gives the input file format, in this case gout stands for gaussian output

-o filename.ac gives the output file

-fo gives the output file format, in this case ac stands for antechamber file format

• example

antechamber -i ch3oh_mk.log -fi gout -o ch3oh_antechamber.ac -fo ac

• which produces output files

[tricia@orris]/Users/tricia/bin/repESP/data/ch3oh $ antechamber -i ch3oh_mk.log -fi gout -o ch3oh_antechamber.ac -fo ac
ch3oh_antechamber.ac
ANTECHAMBER_AC.AC
ANTECHAMBER_AC.AC0
ANTECHAMBER_BOND_TYPE.AC
ANTECHAMBER_BOND_TYPE.AC0
ATOMTYPE.INF

• and the ch3oh_antechamber.ac file looks like the following (the other files are similar!)

[tricia@orris]/Users/tricia/bin/repESP/data/ch3oh $ cat ch3oh_antechamber.ac 
CHARGE      0.00 ( 0 )
Formula: H4 C1 O1 
ATOM      1  C1  MOL     1       0.664  -0.020   0.000  0.000000        c3
ATOM      2  H1  MOL     1       1.083   0.988  -0.001  0.000000        h1
ATOM      3  H2  MOL     1       1.035  -0.543  -0.892  0.000000        h1
ATOM      4  H3  MOL     1       1.035  -0.542   0.892  0.000000        h1
ATOM      5  O1  MOL     1      -0.750   0.122   0.000  0.000000        oh
ATOM      6  H4  MOL     1      -1.134  -0.759   0.000  0.000000        ho
BOND    1    1    2    1     C1   H1
BOND    2    1    3    1     C1   H2
BOND    3    1    4    1     C1   H3
BOND    4    1    5    1     C1   O1
BOND    5    5    6    1     O1   H4
[tricia@orris]/Users/tricia/bin/repESP/data/ch3oh $

two stage restrained fitting process

introduction

• respgen one of the programs inside antechamber fits charges to the ESP
• it carries out two processes equivalencing charges and limiting or constraining charges to a particular value
• typically the constraint is to have charges close to zero
• a typical process includes 2 runs
• in the first run
  • all the charges are fit independently (ie no symmetry is applied)
  • the charges are constrained to zero, but the constraint is very weak 0.0005
• in a second run
  • charges are read in from the first run
  • all atoms are equivalenced, ie symmetry equivalent atoms are constrained to have the same charge
  • the constraint towards zero charge is larger 0.001.

basic instructions

• the two files created file.respout1 and file.respout2 are required for some of Jan's routines
• run the following

respgen -i ch3oh_antechamber.ac -o ch3oh.respin1 -f resp1
respgen -i ch3oh_antechamber.ac -o ch3oh.respin2 -f resp2

• the first script produces the file ch3oh.respin1 which looks like this

Resp charges for organic molecule

 &cntrl

 nmol = 1,
 ihfree = 1,
 ioutopt = 1,
 qwt = 0.00050,

 &end
    1.0
Resp charges for organic molecule
    0    6
    6    0
    1    0
    1    0
    1    0
    8    0
    1    0

• the second script produces the file ch3oh.respin2 which looks like this

Resp charges for organic molecule

 &cntrl

 nmol = 1,
 ihfree = 1,
 ioutopt = 1,
 iqopt = 2,
 qwt =  0.00100,

 &end
    1.0
Resp charges for organic molecule
    0    6
    6    0
    1    0
    1    2
    1    2
    8  -99
    1  -99

more complex options

• there are also more complex options for groups and fitting to multiple structures
• there are also a number of examples
• goto the webpage "http://upjv.q4md-forcefieldtools.org/RED/resp/"
• first block between &cntrl and &end

nmol=number of molecules

ihfree

=0 has all atoms restrained

=1 has hydrogen not restrained, the default

iqopt

=1 reset all initial charges to zero, the default

=2 read new initial charges from -q unit (for the example above -q=1 means read these from ch3oh_respin1)

=3 read new initial charges from -q unit and perform averaging of these charges

ioutopt

=0 normal run

=1 wrtie a restart file of new MEP to -s unit

irstrnt

=0 use old harmonic restraints

=1 use hyperbolic restraints, the default

qwt = xxx gives the strength of the constraint, values typically range from 0.0005 to 0.01

• next sections

wtmol (defines the realtive weight for the structure if multiple structures are to be fit, 1.0 otherwise)

title line

charge iuniq (defines the total charge and total number of atoms)

then one line for each atom giving " atomic-no ivary" in 2I5 format

ivary

=0 fit charge independently

=n fit and equivalenced to that of atom n

=-1 charge frozen at the initial stage , typically read from -q unit

=-99 freeze as well?

• you can run the resp program yourself

resp [-O] -i input -o output -p punch -q qin -t qout -e espot -w qwts -s esout

        -O Overwrite output files if they exist.