AMBER Archive (2006)

Subject: AMBER: An issue with the "multimolecule and multiconformational" resp fit

From: Jason K (jmk9jmk_at_gmail.com)
Date: Tue Apr 11 2006 - 13:16:57 CDT

Dear Amber community,

I am in the process of building amino-acid variants for simulations. Our
interest lies in protonated/deprotonated versions of existing amino acids
for "gas-phase" calculations. After some testing on an arginine residue, we
decided that calculations will be run at a B3LYP/6-31G* level. In any other
respect I am trying to follow the J. Comp. Chem. 1995 paper as well as
possible.

The first problem that we have encountered was building the starting
geometries stated in table II, p. 1362 in the aforementioned paper. It would
really help if the coordinated for these geometries were available.
Furthermore, how significant is it to start the calculations from such a
geometry? Especially for the 'idealised' alpha-helical torsions (-60, -40),
the conformation of backbone atoms is not retained after optimisation. The
C5 geometry seems to 'survive' more frequently.

Now, my main question is about the multi-molecular RESP fitting method. I
have followed all instructions available to extract the ESP data for two
conformations of the residue (it is a C-terminal amidated Alanine) from the
Gaussian output files, catenated the two, then generated resp input files
for the fit. The input for the first fitting step looks like this:

Resp charges for organic molecule

 &cntrl

 nmol = 2,
 ihfree = 1,
 ioutopt = 1,

 &end
    130.0
Resp charges for organic molecule
    0 19
    1 0
    6 0
    1 0
    1 0
    6 0
    8 0
    7 0
    1 0
    6 0
    1 0
    6 0
    8 0
    6 0
    1 0
    1 0
    1 0
    7 0
    1 0
    1 18

    130.0
Resp charges for organic molecule
    0 19
    1 0
    6 0
    1 0
    1 0
    6 0
    8 0
    7 0
    1 0
    6 0
    1 0
    6 0
    8 0
    6 0
    1 0
    1 0
    1 0
    7 0
    1 0
    1 18

    6 0
    1 1 1 2 1 3 1 4 1 5 1 6
    2
    1 1 2 1
    2
    1 2 2 2
    2
    1 3 2 3
    2
    1 4 2 4
    2
    1 5 2 5
    2
    1 6 2 6
    2
    1 7 2 7
    2
    1 8 2 8
    2
    1 9 2 9
    2
    1 10 2 10
    2
    1 11 2 11
    2
    1 12 2 12
    2
    1 13 2 13
    2
    1 14 2 14
    2
    1 15 2 15
    2
    1 16 2 16
    2
    1 17 2 17
    2
    1 18 2 18
    2
    1 19 2 19

With the constraints I'm trying to achieve the following:
- Make all 'identical' atoms from the two conformations equivalent
- Impose a net charge of zero to the capping group (an acetyl moiety - first
six atoms)

Unfortunately though, with the current setup I get the following output
file:

 -----------------------------------------------
      Restrained ESP Fit 2.3 Amber 4.1
 -----------------------------------------------
 Resp charges for organic molecule
 -----------------------------------------------

 inopt = 0 ioutopt = 1
 nmol = 2 iqopt = 0
 ihfree = 1 irstrnt = 1
 iunits = 0 qwt = 0.00050000

 %RESP-I-MULT_MOL, multiple-molecule run of 2 molecules

 Reading input for molecule 1 weight: 130.000
Resp charges for organic molecule

 Total charge (ich): 0
 Number of centers: 19
    1 1 0
    2 6 0
    3 1 0
    4 1 0
    5 6 0
    6 8 0
    7 7 0
    8 1 0
    9 6 0
   10 1 0
   11 6 0
   12 8 0
   13 6 0
   14 1 0
   15 1 0
   16 1 0
   17 7 0
   18 1 0
   19 1 18

 Reading input for molecule 2 weight: 130.000
Resp charges for organic molecule

 Total charge (ich): 0
 Number of centers: 19
   20 1 0
   21 6 0
   22 1 0
   23 1 0
   24 6 0
   25 8 0
   26 7 0
   27 1 0
   28 6 0
   29 1 0
   30 6 0
   31 8 0
   32 6 0
   33 1 0
   34 1 0
   35 1 0
   36 7 0
   37 1 0
   38 1 18
 --------------------------------
 reading mult_mol constraint info
 --------------------------------
    1 1 1 2 1 3 1 4 1 5 1 6
    1 1 2 1
    1 2 2 2
    1 3 2 3
    1 4 2 4
    1 5 2 5
    1 6 2 6
    1 7 2 7
    1 8 2 8
    1 9 2 9
    1 10 2 10
    1 11 2 11
    1 12 2 12
    1 13 2 13
    1 14 2 14
    1 15 2 15
    1 16 2 16
    1 17 2 17
    1 18 2 18
    1 19 2 19

  --------------------
     Atom Ivary
  --------------------
    1 0
    6 1
    1 1
    1 1
    6 1
    8 1
    7 0
    1 0
    6 0
    1 0
    6 0
    8 0
    6 0
    1 0
    1 0
    1 0
    7 0
    1 0
    1 18

    1 1
    6 1
    1 1
    1 1
    6 1
    8 1
    7 7
    1 8
    6 9
    1 10
    6 11
    8 12
    6 13
    1 14
    1 15
    1 16
    7 17
    1 18
    1 18

----------------------------------------------------------------------------

 Total number of atoms = 38
 Weight factor on initial charge restraints= 0.000500

 There are 2 charge constraints

 Reading esp"s for molecule 1
 total number of atoms = 19
 total number of esp points = 5800

 center X Y Z
    1 0.5244048E+01 -0.1457098E+01 -0.3127389E+01
    2 0.5739154E+01 -0.7333327E+00 -0.1252781E+01
    3 0.6891891E+01 -0.2131726E+01 -0.2625642E+00
    4 0.6899441E+01 0.9674244E+00 -0.1487107E+01
    5 0.3460143E+01 -0.8705212E-01 0.3761632E+00
    6 0.3643445E+01 0.2927828E+00 0.2647614E+01
    7 0.1184913E+01 0.1687525E-01 -0.8880635E+00
    8 0.1222708E+01 -0.4359598E-01 -0.2798576E+01
    9 -0.1099770E+01 0.1024093E+01 0.2911255E+00
   10 -0.6254483E+00 0.1184722E+01 0.2301794E+01
   11 -0.3359876E+01 -0.8108380E+00 0.1229399E+00
   12 -0.5531173E+01 -0.7007104E-01 0.3780529E+00
   13 -0.1812204E+01 0.3633803E+01 -0.7387752E+00
   14 -0.3565871E+01 0.4272525E+01 0.1399474E+00
   15 -0.3060959E+00 0.4994410E+01 -0.3381532E+00
   16 -0.2120229E+01 0.3569551E+01 -0.2787238E+01
   17 -0.2757046E+01 -0.3282598E+01 -0.3022484E+00
   18 -0.9447968E+00 -0.3866517E+01 -0.2002032E+00
   19 -0.4153550E+01 -0.4571395E+01 -0.1057169E+00

 Reading esp"s for molecule 2
 total number of atoms = 19
 total number of esp points = 5736

 center X Y Z
    1 -0.4955020E+01 -0.3620564E+01 0.1067614E+01
    2 -0.5644746E+01 -0.1866889E+01 0.2134578E+00
    3 -0.6614181E+01 -0.2314741E+01 -0.1557216E+01
    4 -0.7037462E+01 -0.1005155E+01 0.1477685E+01
    5 -0.3567910E+01 0.4737354E-01 -0.3232244E+00
    6 -0.4013856E+01 0.2116631E+01 -0.1277536E+01
    7 -0.1188755E+01 -0.6802031E+00 0.3362900E+00
    8 -0.7938266E+00 -0.2445213E+01 0.9674584E+00
    9 0.9995687E+00 0.8787887E+00 -0.1909436E+00
   10 0.7558073E+00 0.1729169E+01 -0.2067442E+01
   11 0.3308789E+01 -0.8805783E+00 -0.2041717E+00
   12 0.3218052E+01 -0.3031085E+01 0.6537639E+00
   13 0.1311404E+01 0.3025514E+01 0.1755474E+01
   14 0.2929026E+01 0.4233026E+01 0.1300050E+01
   15 -0.3987813E+00 0.4182050E+01 0.1740356E+01
   16 0.1587294E+01 0.2246943E+01 0.3652759E+01
   17 0.5463092E+01 0.1360640E+00 -0.1171711E+01
   18 0.5499021E+01 0.1844376E+01 -0.2014529E+01
   19 0.7031549E+01 -0.9505511E+00 -0.1232183E+01
 Initial ssvpot = 74200.412

 Number of unique UNfrozen centers= 13

 Non-linear optimization requested.
 qchnge = 0.8392109792E-01
 qchnge = 0.5704251783E-07
 qchnge = 0.3061276458E-12

 Convergence in 2 iterations

Resp charges for organic molecule

          Point Charges Before & After Optimization

    no. At.no. q(init) q(opt) ivary d(rstr)/dq
    1 1 0.000000 0.001696 0 0.000000
    2 6 0.000000 0.001696 1 0.004999
    3 1 0.000000 0.001696 1 0.000000
    4 1 0.000000 0.001696 1 0.000000
    5 6 0.000000 0.001696 1 0.004999
    6 8 0.000000 0.001696 1 0.004999
    7 7 0.000000 -0.536747 0 0.000916
    8 1 0.000000 0.507795 0 0.000000
    9 6 0.000000 -0.297137 0 0.001595
   10 1 0.000000 -0.036016 0 0.000000
   11 6 0.000000 1.199541 0 0.000415
   12 8 0.000000 -0.669359 0 0.000739
   13 6 0.000000 0.245507 0 0.001886
   14 1 0.000000 0.000739 0 0.000000
   15 1 0.000000 -0.049329 0 0.000000
   16 1 0.000000 -0.059168 0 0.000000
   17 7 0.000000 -1.386707 0 0.000360
   18 1 0.000000 0.535351 0 0.000000
   19 1 0.000000 0.535351 18 0.000000

   20 1 0.000000 0.001696 1 0.000000
   21 6 0.000000 0.001696 1 0.004999
   22 1 0.000000 0.001696 1 0.000000
   23 1 0.000000 0.001696 1 0.000000
   24 6 0.000000 0.001696 1 0.004999
   25 8 0.000000 0.001696 1 0.004999
   26 7 0.000000 -0.536747 7 0.000916
   27 1 0.000000 0.507795 8 0.000000
   28 6 0.000000 -0.297137 9 0.001595
   29 1 0.000000 -0.036016 10 0.000000
   30 6 0.000000 1.199541 11 0.000415
   31 8 0.000000 -0.669359 12 0.000739
   32 6 0.000000 0.245507 13 0.001886
   33 1 0.000000 0.000739 14 0.000000
   34 1 0.000000 -0.049329 15 0.000000
   35 1 0.000000 -0.059168 16 0.000000
   36 7 0.000000 -1.386707 17 0.000360
   37 1 0.000000 0.535351 18 0.000000
   38 1 0.000000 0.535351 18 0.000000

 Sum over the calculated charges: 0.000

        Statistics of the fitting:
  The initial sum of squares (ssvpot) 74200.412
  The residual sum of squares (chipot) 74197.016
  The std err of estimate (sqrt(chipot/N)) 3.59657
  ESP relative RMS (SQRT(chipot/ssvpot)) 0.99998

Obviously, the charge constraint for the first 6 atoms does not set the net
charge to zero, but 'forces' every atom to have a charge of (almost) zero.
This makes the fit a bit "irregular" (attributing e.g. unusually high
charges to particular atoms). Is there a way to correct this behaviour? I
have tried different 'spacing' versions of my input file but this is the
best result I've got so far, which is obviously not good enough. I will be
very grateful if anyone could help me on this matter!
I will attached the esp file for your reference. Any advice will be greatly
appreciated.

Jason


  • application/octet-stream attachment: ACM.esp
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