[AMBER] paramfit

From: <stephanie.essafi.ens.fr>
Date: Tue, 24 Jan 2017 14:23:03 +0100

Dear all,

I am new to Amber so I apologise if this is a silly question or if it
has been asked before.

I am trying to use paramfit to fit parameters for a small organic
molecule. I have generated a set of conformations that I believe span
the relevant range of bond lengths, angles and dihedrals. I used a
personal script to generate those conformations. My molecule has
several instances of each bond, angle and dihedral type for which I
want new parameters (to be more precise, I want to create a new atom
type and this atom type appears 4 times in my molecule). Paramfit is
supposed to use all these values to do the fit. However, I have
noticed that, for a given structure, it only takes into account the
smallest value for each bond, angle and dihedral type. The .bondeq,
.angleq, .diheq files all have the same number of line, which
corresponds to the number of conformations. As a result, large bond
lengths, angles and dihedrals are ignored and the fit is poor. How can
I change this?

Many thanks,

Stephanie Essafi
ENS, Paris

This message was sent using IMP, the Internet Messaging Program.

AMBER mailing list
Received on Tue Jan 24 2017 - 05:30:05 PST
Custom Search