AMBER Archive (2004)

Subject: Re: AMBER: AMBER7 : Hybrid macromolecule

From: david.evans_at_ulsop.ac.uk
Date: Mon Sep 13 2004 - 11:30:43 CDT

It is possible to use a covalently bound fragment in this way, but
you need to create your own
parameters for the 'boundary' region. You need a frcmod file with
entries such as
C -ca ? ?
where you choose appropriate values for ? (force constant and bond
length).

It is probably good enough to choose these by analogy with atomtypes
from the gaff forcefield.
e.g. C(parm99) is equivalent to c(gaff) in your example, so you can
can use the c -ca bonding parameter for C -ca, etc, etc. But if these
values are likely to be crucial to your calculation, then maybe you
need to think more carefully about them at some point.

Dave Evans
London School of Pharmacy

---- Message from Guillaume Bollot <Guillaume.Bollot_at_chiorg.unige.ch>
at 2004-09-13 17:54:28 ------
>Dear Users,
>I have an hybrid macromolecule with organic fragments and protein
>fragments. Moreover, I use GAFF (organic part) and PARM99 (protein
part)
>force field but how to combine these two force fields in AMBER 7? Is
it
>possible?
>
>Error message in Xleap after the CHECK command :
>Could not find bond paramater for : C -ca
>....
>Could not find angle parameter for : C - ca -ca
>....etc...
>
>Someone could help me? Thanks a lot in advance.
>
>Bollot Guillaume, University of Geneva.
>
>--------------------------------------------------------------------- 

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