AMBER Archive (2005)

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

From: FyD (fyd_at_u-picardie.fr)
Date: Mon Oct 24 2005 - 03:44:31 CDT

Quoting Cenk Andac <cenk_andac_at_yahoo.com>:

> I have determined RESP charges for a Cu.4H2O complex
> by REDII and GAMESS.

Check the RMS & RRMS in the RESP output1 and/or output2 !

> I would like to use RESP charges for TP3 from Cornell
> at al. in the copper complex and run a restrained RESP
> job as suggested in RED II manual.(I do not have
> access to AMBER at this moment, but as far as I
> remember partial charges for TP3 water ought to be
> about +0.4 for H and -0.8 for O.)

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

> However, how input1 (and input2 ?) should be modified
> to run the resp jobs above is not clearly exemplified
> in RED II manual.

You did a 12 mol. orientation RESP fit ? Right ?

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
- Freeze all in input2

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.
This is automatically done in R.E.D.-III

> Therefore, I am sending you my GAMESS outputs as an
> attachment in zip format for you to see.

I am not sure, it is a good idea to send your files in the AMBER mailing list.

> 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

Regards, Francois

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