Re: [AMBER] Implementing parameterized heme?

From: Pengfei Li <ambermailpengfei.gmail.com>
Date: Wed, 29 Oct 2014 15:44:02 -0400

Another thing is about editing the molecule in xleap.
It seems xleap will treat the name molecule name in prep file as standard.

For example, in the heme_all.in file, we can check the molecule name in the line:
"HEM INT 0", HEM is the molecule name. So when you try to edit that molecule in xleap,
You should use "edit HEM" command.

HTH,
Pengfei

On Oct 29, 2014, at 3:35 PM, Pengfei Li <ambermailpengfei.gmail.com> wrote:

> 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 onů" 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
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>

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Received on Wed Oct 29 2014 - 13:00:03 PDT
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