From: Eduardo Mendez <>
Date: Tue, 18 Sep 2007 17:52:18 -0600

Hello Francois

I am trying to run your program, however the perl script can not find
the games
software. Where do I specify the local directory?.
I am also trying to specify higher level of theory for gaussian with
no luck (this belongs to another forum I guess)

           gamess.0n.x (n = 0->9)
[ OK ]
                   At least one GAMESS-US binary is missing !
                   Use PC-GAMESS instead of GAMESS-US...

FyD wrote:
> Quoting Eduardo Mendez <>:
>> I was wondering if anyone could share the amber parameter files for
>> oxalate. I did gaussian calculations to get the mulliken charges,
>> however, to my dismay, gaussian gives me an isomer, which
>> is not in the planar conformation one would expect it to be :(
>> Any idea were can I find a library site other than
>> ???
> - Yes, I saw this 'strange' conformation. Just try to re-run the job
> using higher basis sets with DFT + diffusion function(s)
> (B3LYP/6-31+G** or even higher...), using also different initial
> structures (planar & not planar). Now this conformation might be the
> right one. This could be explained by the two negative charges which
> would be too close if the structure is planar... Did you look at the
> frequencies ? They are all positive. This means this a real minimum at
> the theory level used.
> - AMBER FFs use RESP charges, not mulliken charges.
> - Using the data I sent you, use the .mol2 file to add the FF atom
> type (very simple for oxalate: O2, C, C, O2). Then, generate a
> torsional profile for the O-C-C-O dihedral with structures generated
> every 30 deg. Get the Eqm and Emm energy values, and fit Emm to Eqm.
> (We have FFParmDev that does the job, but it is not yet ready to be
> released; I can do it but not now).
> regards, Francois
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Received on Wed Sep 19 2007 - 06:07:43 PDT
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