AMBER Archive (2007)

Subject: Re: AMBER: CONFIGURATION FILE FOR OXALATE C2O4^2-

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Thu Sep 20 2007 - 06:54:23 CDT

Quoting Eduardo Mendez <pckboy_at_gmail.com>:

> Here is what I got using ANTECHAMBER to get the resp charges.
> I used as you suggested, a higher level of theory(B3YLP and so on.)
> obtaining a planar geometry for oxalate...

OK thanks for the feed back...

> CHARGE -2.00 Formula: C2 O4 ATOM 1 C1 OXL 1 0.000
> 0.000 0.821 0.727276 c
> ATOM 2 C2 OXL 1 0.000 0.000 -0.821 0.727276 c
> ATOM 3 O1 OXL 1 -0.001 1.124 1.392 -0.863638 o
> ATOM 4 O2 OXL 1 -0.001 -1.124 -1.392 -0.863638 o
> ATOM 5 O3 OXL 1 0.001 -1.124 1.392 -0.863638 o
> ATOM 6 O4 OXL 1 0.001 1.124 -1.392 -0.863638 o
> BOND 1 1 2 0 C1 C2
> BOND 2 1 3 0 C1 O1
> BOND 3 1 5 0 C1 O3
> BOND 4 2 4 0 C2 O2
> BOND 5 2 6 0 C2 O4
>
> The PC GAMESS version is broken :(, only got the one for chemoffice
> ...and the source code gave me a headache. Oh my!.

So get the PC-GAMESS version for LINUX without that chemoffice, you
will save computer time...

> Here it is the output from GAMESS for the RESP charges:
> 0.735501 0.732186 -0.867237 -0.866606 -0.867237 -0.866606

The equivalencing procedure is wrong because of the atom names
available in your P2N. Please read the tutorial.

> and here is the p2n input
> REMARK
> REMARK TITLE MOLECULE
> REMARK CHARGE-VALUE -2
> REMARK MULTIPLICITY-VALUE 1
> REMARK
> ATOM 1 C1 OXL 557 0.747 0.000 0.002 C1
> ATOM 2 C2 OXL 557 -0.747 0.000 0.000 C2
> ATOM 3 O3 OXL 557 1.385 -1.105 0.001 O1
> ATOM 4 O4 OXL 557 -1.385 -1.105 -0.002 O2
> ATOM 5 O5 OXL 557 1.385 1.105 -0.002 O3
> ATOM 6 O6 OXL 557 -1.385 1.105 0.001 O4

                ^^
           Wrong atom names; They should be:
                C1
                C1
                O2
                O2
                O2
                O2

regards, Francois

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