Dear Ross,
Thank you so much. I will try it again carefully. I see that the frcmod
file contains some comments which i guess the articles from which these
parameters for cu has been extracted. Could you please suggest me some
references that discuss about ff parameters of cu compatible with amber ff.
Thanks,
Bala
On Mon, Mar 26, 2012 at 6:37 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
> Dear Bala,
>
> You are not following the tutorial properly. Please read it again
> carefully.
> You need to load both the lib file and a frcmod file containing the
> parameters for copper and any related bonds, angles, dihedrals etc.
>
> See the beginning of section4.
>
> http://ambermd.org/tutorials/advanced/tutorial1_orig/section4.htm
>
> All the best
> Ross
>
> > -----Original Message-----
> > From: Bala subramanian [mailto:bala.biophysics.gmail.com]
> > Sent: Monday, March 26, 2012 8:24 AM
> > To: AMBER Mailing List
> > Subject: [AMBER] TUTORIAL A1: Protein that Contains Non-Standard
> > Residues
> >
> > Hello,
> > I am trying to reproduce tutorial A1. In section two, it is shown how
> > to
> > use leap to create a new residue (for copper). I followed the same
> > procedure as given in the tutorial. creating a unit called CUA -
> > editing
> > the copper atom to define type and charge - saving the library as
> > cua.lib.
> >
> > After creating a new residue called CUA and saving the lib file, I quit
> > the
> > leap and then started it again. Then i tried to create a prmtop and crd
> > files for copper but leap shows me the following error.
> >
> > > loadoff cua.lib
> > Loading library: ./cua.lib
> > Loading: CUA
> > > saveamberparm CUA cua.top cua.crd
> > Checking Unit.
> > WARNING: The unperturbed charge of the unit: 1.000000 is not zero.
> > WARNING: The perturbed charge: 1.000000 is not zero.
> > -- ignoring the warnings.
> >
> > Building topology.
> > Building atom parameters.
> > For atom: .R<CUA 100>.A<CU 1> Could not find type: CU
> > Parameter file was not saved.
> >
> > Herewith i have attached the leap.log file and the cua.lib (renamed as
> > just
> > cua) files. Kindly write me what is going wrong here.
> >
> > Thanks,
> > --
> > C. Balasubramanian
>
>
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
C. Balasubramanian
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Received on Mon Mar 26 2012 - 12:30:04 PDT
