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From: Cenk Andac <cenk_andac.yahoo.com>

Date: Mon, 24 Oct 2005 09:43:36 -0700 (PDT)

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.yahoo.com

__________________________________

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http://www.rosswalker.co.uk/adsense_alternatives/

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

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Received on Mon Oct 24 2005 - 17:53:00 PDT

Date: Mon, 24 Oct 2005 09:43:36 -0700 (PDT)

Hi Francois,

I guess I am having difficulty understanding your

previous E-Mail since I am not experienced on the

freezing stuff you mention

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?

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?

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?

Manually in a gamess input? which one? How?

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.yahoo.com

__________________________________

Yahoo! Mail - PC Magazine Editors' Choice 2005

http://www.rosswalker.co.uk/adsense_alternatives/

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

The AMBER Mail Reflector

To post, send mail to amber.scripps.edu

To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu

Received on Mon Oct 24 2005 - 17:53:00 PDT

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