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 - 11:12:30 CDT

Hi Francois,

Thanks for replying.

Would lt be possible to have a beta version of REDIII
if possible ?

regards,

jenk.

--- FyD <fyd_at_u-picardie.fr> wrote:

> 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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