AMBER Archive (2005)

Subject: RE: AMBER: How to modify force constants and equalibrium values for standard residues

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Thu Jun 16 2005 - 16:05:33 CDT

You can create your own frcmod file with parameters in it that will override
the default parameters from the parm file.

Alternatively you could copy the default parm.dat file - e.g. parm99.dat to
your home directory, modify it and then load it into leap with the
loadamberparams command. It will then overide all of the default parm99.dat
parameters.

Note, this will change the parameters for every residue. If you just want to
change it for one residue and leave all the others alone you will need to
create a non-standard residue and define new atom types for each of the
atoms in this residue.

All the best
Ross

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> -----Original Message-----
> From: owner-amber_at_scripps.edu
> [mailto:owner-amber_at_scripps.edu] On Behalf Of Li Su
> Sent: 16 June 2005 06:31
> To: amber_at_scripps.edu
> Subject: AMBER: How to modify force constants and equalibrium
> values for standard residues
>
> Dear amber users,
>
> I'm wondering if there is someway for me to modify force
> constants and
> equalibrium values for standard residues besides directly
> change the prmtop
> file. If it is the only way (the amber script I'm using is
> installed on some
> mainframe,so I can't modify it' s library), where can I find some
> straightforward examples? Thank you in advance.
>
>
> Best wishes,
>
> Li
>
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