Thank you!!
rdparm actually gives "missing" improper:
B 62: 1.000 3.14 2.0 :1.C2 :1.H21 :1.N2 :1.H22
(20,22,21,23)
I hope that parmchk has no any other limitations, because it is really
helpful program...
On Wed, Jun 23, 2010 at 3:05 AM, case <case.biomaps.rutgers.edu> wrote:
> On Tue, Jun 22, 2010, Dmitry Nilov wrote:
>
> > Learning guanosine parametrization in ff99, I've been confused with one
> > observation about impropers.
> >
> > To extract guanosine parameters I've done the follows:
> > 1)creating Mol2:
> > tleap -s -f leaprc.ff99SB
> > savemol2 DGN dgn.mol2 1
> > 2)extracting params:
> > parmchk -i dgn.mol2 -f mol2 -o dgn_params.frcmod -p
> > /home/nilov/amber10/dat/leap/parm/parm99.dat -a Y
>
> Please check if this is this is just a limitation of parmchk. That is, run
> rdparm and use the printDihdedrals command to see if the prmtop file (which
> you would need to create, I guess) has the desired improper.
>
> ...thanks....dac
>
>
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--
Dmitry Nilov,
Lomonosov Moscow State University
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Received on Wed Jun 23 2010 - 02:30:04 PDT
