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 Fri Jan 04 2013 - 11:00:03 PST
