Re: [AMBER] improper for NH2 group in guanosine

From: case <>
Date: Tue, 22 Jun 2010 19:05:01 -0400

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.


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Received on Tue Jun 22 2010 - 16:30:03 PDT
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