Hi,
Thanks very much to both of you for your help. I'm not that well versed in
creating the parameter files and had failed to source the frcmod properly.
I rectified this and the parameter files were created properly. :)
Best regards,
g
On 4 January 2013 18:50, David A Case <case.biomaps.rutgers.edu> wrote:
> On Fri, Jan 04, 2013, Girish wrote:
>
> > >
> > > I'm trying to parametrise some of the HIV-1 protease inhibitors and am
> > > having a problem with TMC-126.
> > > http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?sid=17396648
> > >
> > > I used the RESP methodology to generate the partial charges via the RED
> > > program using 6-31G* basis set. Using antechamber in AMBER 10, I
> generated
> > > a mol2 file and used parmchk to create a frcmod file. The latter is as
> > > follows:
> > > $AMBERHOME/exe/antechamber -i Mol_m1-o1.mol2 -fi mol2 -o TMC-126.mol2
> -fo
> > > mol2 -s 2
> > >
> > > parmchk -i TMC-126.mol2 -o frcmod
> > ###################
> > remark goes here
> > MASS
> >
> > BOND
> > n3-sy 353.80 1.632 same as n3-s6
> >
> > ANGLE
> > c3-n3-sy 63.900 115.810 same as c3-n3-s6
> > n3-sy-o 72.900 106.800 same as n3-s6-o
> > n3-sy-ca 39.678 103.680 Calculated with empirical approach
> >
> > DIHE
> >
> > IMPROPER
> > n -o -c -os 10.5 180.0 2.0 General
> > improper torsional angle (2 general atom types)
> > ca-ca-ca-ha 1.1 180.0 2.0 General
> > improper torsional angle (2 general atom types)
> > ca-ca-ca-sy 1.1 180.0 2.0 Using default
> > value
> > ca-ca-ca-os 1.1 180.0 2.0 Using default
> > value
> >
> > NONBON
> > ###################
>
>
> This is correct, but it looks like you never loaded the "frcmod" file into
> LEaP in the next step.
>
> > > Could not find bond parameter for: n3 - sy
>
> Note that the n3-sy force constant is indeed in the frcmod file you created
> during the parmchk step--looks like you just need to get that loaded.
>
> ...maybe I am missing something....hope this helps....dac
>
>
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Received on Sat Jan 05 2013 - 11:30:02 PST
