AMBER Archive (2005)

Subject: Re: Modification of GAMESS outputs for resp jobs Re: AMBER: Cu++ and RED

From: Cenk Andac (cenk_andac_at_yahoo.com)
Date: Mon Oct 24 2005 - 11:43:36 CDT

Hi Francois,

I guess I am having difficulty understanding your
previous E-Mail since I am not experienced on the
freezing stuff you mention

>
> Check the RMS & RRMS in the RESP output1 and/or
> output2 !
RMS values at the end of Output 1:
---------------------------------------------
  Statistics of the fitting:
  The initial sum of squares (ssvpot)
  161.277
  The residual sum of squares (chipot)
    0.015
  The std err of estimate (sqrt(chipot/N))
  0.00433
  ESP relative RMS (SQRT(chipot/ssvpot))
  0.00973

-------------------------------
RMS values at the end of output 2:

      Statistics of the fitting:
  The initial sum of squares (ssvpot)
  161.277
  The residual sum of squares (chipot)
    0.015
  The std err of estimate (sqrt(chipot/N))
  0.00433
  ESP relative RMS (SQRT(chipot/ssvpot))
  0.00973
------------------------------------

Are these values good?

> TIP3P charges
> O -.8340
> H .4170
>
> > resp -O -i input1 -e espot -o output1 -p punch1 -q
> > qout -t qout1 -w qwts -s esout
> >
> > resp -O -i input2 -e espot -o output2 -p punch2 -q
> > qout1 -t qout2 -w qwts -s esout
>
> OK, taken from
> http://www.u-picardie.fr/labo/lbpd/RED/FAQ-I.htm#27
>
> Well I would test the Kollman' group strategy 1st,
> checking the RMS/RRMS as said
> above:
> - you should do the O and H equivalencing in the 1st
> input
Here is a part of input 1:

  1.0
 c4w
   1 13
   8 0
   1 0
   1 2
   8 0
   1 0
   1 5
   8 0
   1 0
   1 8
   8 0
   1 0
   1 11
  29 0

Ok. What do I do here for the O and H equivalencing
you mentioned?

> - Freeze all in input2

Here is a part of input 2:

 1.0
 c4w
   1 13
   8 -1
   1 -1
   1 -1
   8 -1
   1 -1
   1 -1
   8 -1
   1 -1
   1 -1
   8 -1
   1 -1
   1 -1
  29 -1

Again, what do I do to freeze stuff here ? add zeros
intead of -1?

>
> Another strategy would be to add intra-molecular
> restraint on the O and H charge
> values to force them to take the TIP3P charge
> values... You can do it manually.
Manually in a gamess input? which one? How?

> This is automatically done in R.E.D.-III
>
> > I have another question. How do I convert the new
> resp
> > output to mol2 format?
>
> Manually: Your model is small it is not a problem.
> It is done automatically in R.E.D.-III
>

I guess it would be a good idea to have a beta version
of REDIII sometime from you.

best regards,

jenk.

Cenk Andac, M.S., Ph.D. Dissertator
at the University of Wisconsin-Madison
 
Currently a faculty candidate in Turkey
Address:
Guleryuz cad. 37/15, Ankara, Turkey
90-(312)-4281941
E-Mail:cenk_andac_at_yahoo.com

        
                
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