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)
rungms
[ NOT FOUND ]
gamess.0n.x (n = 0->9)
[ NOT FOUND ]
ddikick.x
[ NOT FOUND ]
pcgamess.exe
[ OK ]
At least one GAMESS-US binary is missing !
Use PC-GAMESS instead of GAMESS-US...
FyD wrote:
> Quoting Eduardo Mendez <pckboy.gmail.com>:
>
>> 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
>> http://pharmacy.man.ac.uk/amber/ ???
>
> - 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
