AMBER Archive (2008)

Subject: Re: AMBER: REDvIII_I_lack_of_charges_in_mol2

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Sat Oct 18 2008 - 06:54:56 CDT

Quoting Karol Kaszuba <karolkaszub_at_gmail.com>:

> I am trying to derive RESP A1 charges. I am using Gaussian.
> RED fnishes normally without any errors, (RED.log is absolutely OK)

This is strange. R.E.D. performs many checkings: It should have
detected the problem... Just to be sure: did you apply the bug fixes
available from the R.E.D. web site ?

> 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

=> Those 2 files are for the second RESP stage: This means the problem
appends in the first RESP stage.

> 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

All what you describe in the "qout", "output" files means you have a
problem in the first fitting stage.

> 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.

Do you use any particular constraints in your fit ? i.e. do you derive
charge values for a particular molecular fragment using the INTRA-MCC
or/and the INTER-MCC keyword (INTER-MEQ keywords ?)?
or do you derive charge values for a whole molecule ?

Could you describe a little more what you are trying to do with R.E.D.-III ?

regards, Francois

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu