AMBER Archive (2008)

Subject: AMBER: REDvIII_I_lack_of_charges_in_mol2

From: Karol Kaszuba (karolkaszub_at_gmail.com)
Date: Sat Oct 18 2008 - 06:08:53 CDT

Hello,

I am trying to derive RESP A1 charges.
I am using Gaussian.
RED fnishes normally without any errors, (RED.log is absolutely OK) however
the .mol2 file doesn't have any charges - all columns are 0.000.
I started digging and I figure out that:

1) Instead off 16 files after RED execution I have only 14.
    The missing files are:
    punch2_m1
    qout2_m1

2) In the file: output1_m1 I could see this warning:
    WARNING: Restraints were requested, but the restraint weights were all
zero,
    then:
              Point Charges Before & After Optimization

    no. At.no. q(init) q(opt) ivary d(rstr)/dq
    1 7 0.000000 nan 0 nan
    2 1 0.000000 nan 0 0.000000
    3 6 0.000000 nan 0 nan
    4 1 0.000000 nan 0 0.000000
    5 6 0.000000 nan 0 nan
    6 1 0.000000 nan 0 0.000000
    7 1 0.000000 nan 0 0.000000
    8 6 0.000000 nan 0 nan
    9 7 0.000000 nan 0 nan
   10 1 0.000000 nan 0 0.000000

 Sum over the calculated charges: nan

        Statistics of the fitting:
  The initial sum of squares (ssvpot) 21.206
  The residual sum of squares (chipot) nan
  The std err of estimate (sqrt(chipot/N)) nan
  ESP relative RMS (SQRT(chipot/ssvpot)) nan

 Center of Mass (Angst.):

 X = 0.00000 Y = 0.00000 Z = 0.00000

 Dipole (Debye):

 X = nan Y = nan Z = nan

 Dipole Moment (Debye)= nan

 Quadrupole (Debye*Angst.):

 Qxx = nan QYY = nan QZZ = nan
 Qxy = nan QXZ = nan QYZ = nan

3) In the file output2_m1:

   Charge on the molecule(ich) = -1
 Total number of atoms (iuniq) = 10
 Weight factor on initial charge restraints(qwt)= 0.10000E-02

  there are 48 charge constraints:

     1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0
            0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
            0 0 0 0 0 0 0 1
     2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0
            0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1
            0 0 0 0 1 0 0 1
     3 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0
            0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
            0 0 0 0 0 0 0 1
     4 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0
            0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0
            1 0 0 0 0 0 0 1
     5 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0
            0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
            0 0 0 0 0 0 0 1
     6 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0 0
            0 1 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0
            0 0 0 0 0 0 1 1
     7 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0
            0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
            0 0 0 0 0 0 0 1
     8 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0
            0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0
            0 0 0 0 0 0 0 1
     9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
            0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
            0 0 0 0 0 0 0 1
    10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
            0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
            0 0 0 0 0 0 0 1

  Unit 10 Error on OPEN: ÿÿÿÿt_m1 ÿÿÿÿ
ÿÿÿÿÿÿÿÿ ÿÿÿÿÿÿÿÿ

4) In file punch1_m1:

   iqopt irstrnt ihfree qwt
  1 -1 1 0.000500

 rel.rms dipole mom Qxx Qyy Qzz
        nan nan nan nan nan

          Point charges before & after optimization
    NO At.No. q0 q(opt) IVARY d(rstr)/dq
     1 7 0.000000 nan 0 nan
     2 1 0.000000 nan 0 0.000000
     3 6 0.000000 nan 0 nan
     4 1 0.000000 nan 0 0.000000
     5 6 0.000000 nan 0 nan
     6 1 0.000000 nan 0 0.000000
     7 1 0.000000 nan 0 0.000000
     8 6 0.000000 nan 0 nan
     9 7 0.000000 nan 0 nan
    10 1 0.000000 nan 0 0.000000

        Statistics of the fitting:
  The initial sum of squares (ssvpot) 21.206
  The residual sum of squares (chipot) nan
  The std err of estimate (sqrt(chipot/N)) nan
  ESP relative RMS (SQRT(chipot/ssvpot)) nan

 Dipole Moment (Debye)= nan

  5) In the file: qout1_m1
             nan nan nan nan nan nan
nan nan
       nan nan

    I checked the gaussian log: JOB2-gau_m1-1-1.log - and I do not see any
warnings.
    The molecule for which I am trying to compute the charges is quite big:
107 atoms.
    The charge is -1 and multiplicity is set to 2.

   Any help will be appreciated.

   Thank you in advance,
    Karol Kaszuba

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