Hi Kevin,
It seems that you are using the all atom parameters of heme with the ff03-united-atom force field.
There is also a united atom version of the heme parameters in that website.
It would be better for you to use that one.
I checked the heme parameter files online, it seems they have a old fashion style which is different
from the prep file nowadays use. "no charges read on�" this error may comes from that reason.
You can manually change the file from old style to the new one.
Here is an example with the new style:
http://ambermd.org/antechamber/EFZ_sybyl_resp_gaff.prepc
The mainly difference is the place of the charge information.
Feel free to ask if you have other questions.
HTH,
Pengfei
On Oct 29, 2014, at 1:21 PM, Kevin Murphy <km6.pdx.edu> wrote:
> Hi,
>
> 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:
> http://www.pharmacy.manchester.ac.uk/bryce/amber/.
>
> 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
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Received on Wed Oct 29 2014 - 13:00:02 PDT
