parmchk may be a useful utility here. If you just issue the command
"parmchk" it will print out usage instructions.
Good luck!
Jason
On Wed, Jan 19, 2011 at 12:42 PM, Sangita Kachhap <sangita.imtech.res.in>wrote:
> Hello all
>
> I have to generate parameter for phospho aspartate.
> For this I have download sdf file for pohspho aspartate from PDB,converted
> it
> into pdb
> format using openbabel.
>
> Using antechamber I have generated prepin file and to get the mising
> parameter
> generate
> frcmod file.In frcmod file there is only one missing parameter
>
> remark goes here
> MASS
>
> BOND
>
> ANGLE
>
> DIHE
>
> IMPROPER
> c3-o -c -os 10.5 180.0 2.0 General
> improper
> torsional angle (2 general atom types)
>
> NONBON
>
> When I load prepin and check the unit it shows missing parameter for
>
> Checking for bond parameters.
> Could not find bond parameter for: o - c
> Could not find bond parameter for: c - h4
> Could not find bond parameter for: c - c3
> Could not find bond parameter for: c3 - n3
> Could not find bond parameter for: c3 - h1
> Could not find bond parameter for: c3 - c3
> Could not find bond parameter for: n3 - hn
> Checking for angle parameters.
> Could not find angle parameter: o - c - h4
> Could not find angle parameter: o - c - c3
> Could not find angle parameter: c - c3 - n3
> Could not find angle parameter: c - c3 - h1
> Could not find angle parameter: c - c3 - c3
> Could not find angle parameter: h4 - c - c3
> Could not find angle parameter: c3 - n3 - hn
>
>
> But in frcmod file their is not angle and bond parameter so I am not able
> to
> generate parameter file.
>
>
> When I repeat the same for ATP I successfully generate lib file and also
> prmtop
> and inpcrd file for
> protein having ATP.
>
> So can anybody suggest me why missing parameters are not writing in frcmod
> file?
>
>
> Here I am attaching following files:
> sdf
> pdb(converted by babel)
> prepin
>
>
>
> With regard
> Sangita Kachhap
> JRF
> BIC,IMTECH
> CHANDIGARH
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Wed Jan 19 2011 - 10:30:05 PST
