[AMBER] Implementing parameterized heme?

From: Kevin Murphy <km6.pdx.edu>
Date: Wed, 29 Oct 2014 10:21:21 -0700


I'm new to the AMBER field. I'm attempting the dynamic simulation of a
drug's interaction with heme in solution. I'm trying to use the
parameterized heme as available here:

The following is my input:

> source leaprc.ff03ua
>> (parameters and libraries are successfully loaded)
> loadamberparams "~/frcmod.hemall"
>> Loading parameters: ~/frcmod.hemall
>> Reading force field modification type file (frcmod)
>> Reading title:
>> Heme parameters
> heme = loadamberprep "~/heme_all.in"
>> Loading Prep file: ~/heme_all.in
>> (no charges read on atoms lines in Heme residue ALL ATOM, Yves
names, Bayly-modified)

When I attempt to visualize, via "edit heme", I get ...

Creating a new, empty UNIT "heme"

... and an empty visualization window.

This is where I'm stuck.

Thank you in advance for any help you can offer!

Kevin Murphy
AMBER mailing list
Received on Wed Oct 29 2014 - 10:30:03 PDT
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