Re: [AMBER] atom types error

From: Urszula Uciechowska <urszula.uciechowska.chem.umu.se>
Date: Thu, 1 Dec 2011 14:25:32 +0100

Dear Francois,

I attached you my mol2 file, please propose me the atom types,

Thank you in advance

Urszula
________________________________________
Von: FyD [fyd.q4md-forcefieldtools.org]
Gesendet: Donnerstag, 1. Dezember 2011 13:20
An: AMBER Mailing List
Betreff: Re: [AMBER] atom types error

Dear Urszula,

Simply open the parm99.dat file . $AMBERHOME/dat/leap/parm/ and:

gedit $AMBERHOME/dat/leap/parm/parm99.dat &

Check if the CC-CR force field parameter (bond) do exist: no
but CC-CW does exist:
CC-CW 518.0 1.371 JCC,7,(1986),230; HIS(epsilon)

I wonder if you did not invert the CR and CW atom types in your cycle:
look at their definition in parm99.dat

then, for sure S-CW and/or S-CR does not exist ;-) you will have to
create this FF parameter by analogy to an existing FF parameter; just
copy/cut the FF constant in this case (this is a cycle) and take the
equilibrium value from the QM geometry optimization.

or send me your mol2 file and I will propose you atom types & a frcmod file...

regards, Francois


> I have still problems with adding correct FF atom types to my mol2
> file, (attached)
>
> > check x
> Checking 'x'....
> Checking parameters for unit 'x'.
> Checking for bond parameters.
> Could not find bond parameter for: CC - CR
> Could not find bond parameter for: CR - S
> Could not find bond parameter for: S - CW
> Could not find bond parameter for: CW - NB
> Checking for angle parameters.
> Could not find angle parameter: CT - CC - CR
> Could not find angle parameter: CC - CR - H5
> Could not find angle parameter: CC - CR - S
> Could not find angle parameter: CC - NB - CW
> Could not find angle parameter: CR - CC - NB
> Could not find angle parameter: CR - S - CW
> Could not find angle parameter: H5 - CR - S
> Could not find angle parameter: S - CW - H4
> Could not find angle parameter: S - CW - NB
> Could not find angle parameter: H4 - CW - NB
> There are missing parameters.
> Unit is OK.
>> quit
>
> this is what i am getting, I also run antechamber for the molecule
> and changed the CR and CW to CD but it did not help much,
>
> Can you suggest me something here?
>
> /Urszula



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Received on Thu Dec 01 2011 - 05:30:05 PST
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