The prefered way to do all these is to create a modified parm.dat file
where you can define new atom types, new bonds, etc.
Search the directory $AMBERHOME/dat/leap/parm (or its cousins). There
should be couple of files in that directory which can be used as
examples.
yong
> -----Original Message-----
> From: owner-amber.scripps.edu
> [mailto:owner-amber.scripps.edu] On Behalf Of Herbert Georg
> Sent: Friday, October 24, 2003 2:52 PM
> To: amber.scripps.edu
> Subject: Re: AMBER: prmtop file format
>
>
> Ok Yong, I've got it. Now it matched perfectly. With this
> information,
> can I just change the equilibrium values of bond lenghts in the flag
> ¨%FLAG BOND_EQUIL_VALUE¨ in prmtop file so to get it suitable to my
> molecule?? can I change the force constants as well?? What if I split
> the types of bonds, for example to diferentiate the bonds in
> an aromatic
> ring to produce a quinone character?
> If I cando all of that with no trouble, where can I find
> parameters for
> bond force costants and bond equilibrium values that differentiate
> between single and double bonds??
>
> Thanks
> Herbert
>
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Received on Mon Oct 27 2003 - 07:53:02 PST
