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: Tue Oct 25 2005 - 00:58:56 CDT

Quoting Cenk Andac <cenk_andac_at_yahoo.com>:

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

means keep in the step 2 the charge values from the step 1.
i.e. put -1 in the input

> Are these values good?

Yes

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

    1 13
    8 0
    1 0
    1 2
    8 1
    1 2
    1 2
    8 1
    1 2
    1 2
    8 1
    1 2
    1 2
   29 0

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

yes

> Manually in a gamess input? which one? How?

No in the RESP input stage 1, again freeze all in stage 2
please, read the RESP documentation about intra-molecular restraints

- jump a line
- charge value for the group of atoms; nb of atoms in this group
- mol nb, atom number

in your case, it could be something like:

 -.8340 1
    1 1
   .4170 1
    1 2
   .4170 1
    1 3

etc for all TIP3P wat. in molecule 1...
Same idea for molecule 2 to 12

Concerning inter-molecule charge equivalencing keep only the value for the atom3
which have a zero in the atom set up i.e. the 1st, 2nd and last atoms, see
above...

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

The problem is that a new manual has to be written with new tutorials to explain
how to use it. I cannot do it now, impossible, to many stuffs to do before
that...

Best regards, Francois

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