There is no need to add them to gaff.dat Use parmchk to create an frcmod
with the missing parameters for your ligand. Then load this frcmod (you may
have to edit it if parmchk can't find similar parameters) when you build
your prmtop in leap.
HTH,
Jason
On Thu, Aug 4, 2011 at 12:03 PM, Shulin Zhuang <shulin.zhuang.gmail.com>wrote:
> Dear All,
>
> When I use ambertool to prepare the parameters of my ligand, I can get the
> new.frcmod, however, I could not save the prmtop files. How shoul I do?
> Thanks for your help!
>
> It seems that gaff.dat does not contains such parameters, how to add them
> to
> gaff.dat? The attached lig.pdb contains 4 Cl atom, two of which are in
> pheonic ring and another two are in a single SP2 Carbon C.
>
>
> The errors:
> Building proper torsion parameters.
> ** No torsion terms for ca-ca-ce-c2
> ** No torsion terms for ca-ca-ce-c2
> ** No torsion terms for ca-ca-ce-ca
> ** No torsion terms for ca-ca-ce-c2
> ** No torsion terms for ca-ca-ce-ca
> ** No torsion terms for ca-ca-ce-c2
> ** No torsion terms for ca-ce-ca-ca
> ** No torsion terms for ca-ce-ca-ca
>
>
>
> The content of frcmod:
> remark goes here
> MASS
>
> BOND
>
> ANGLE
>
> DIHE
> ca-ce-ca-ca 1 2.550 180.000 2.000 same as X
> -c2-ca-X
> ca-ca-ce-c2 1 6.650 180.000 2.000 same as X
> -c2-ce-X
>
> IMPROPER
> ca-ca-ca-ce 1.1 180.0 2.0 Using default
> value
> ca-ca-ca-ha 1.1 180.0 2.0 General
> improper
> torsional angle (2 general atom types)
> c2-ca-ce-ca 1.1 180.0 2.0 Using default
> value
> ce-cl-c2-cl 1.1 180.0 2.0 Using default
> value
>
> NONBON
>
> Great thanks
>
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Aug 04 2011 - 09:30:05 PDT
