Hi Yarrow,
On Oct 29, 2014, at 8:34 PM, Yarrow Madrona <Acacia.Madrona.ucsf.edu> wrote:
>
> But I receive the following error at the very end for all atoms in the heme:
>
> FATAL: Atom .R<HIE 16>.A<HD1 18> does not have a type.
>
> FATAL: Atom .R<HEM 149>.A<CAA 1> does not have a type.
>
These errors are because there is no agreement between the pdb file and the library files (prep or lib files)
you are using. The pdb file and lib/prep file should be have a one to one relationship for the atom names
and residue name in a specific residue.
tleap will treat all the HIS residue as HIE in default.
HIE should not have HD1 atom since its protonated site is epsilon site, your pdb file has HD1 in HIS residue
caused you have the first error. You need to change the residue name of HIS which is actually HID or HIP
before using tleap.
The second error comes from the similar thing: there is a CAA atom in your pdb file but there is no such an atom
in the heme_uni.in file. You need to make sure they are consistent with each other before the modeling. Also,
usually the pdb file is full atom based, but the prep file you are using is the united atom based. For the situation
you met, you can use the full atom based prep file (you can download from the same website) or change the heme
residue in your pdb file to united atom based by yourself.
> etc….
>
> The parameters are not written. Somehow I need to enter the types for each
> atom with charge I think. Any help would be appreciated.
>
> -Yarrow
>
HTH,
Pengfei
> On Wed, Oct 29, 2014 at 12:44 PM, Pengfei Li <ambermailpengfei.gmail.com>
> wrote:
>
>> 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 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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>>>> AMBER.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
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>>
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Received on Thu Oct 30 2014 - 12:30:02 PDT
