Hi Ben,
Thanks for the response. Sorry, I was away and didn't have a chance to
read your message. I have attached the RESP input files that MCPB
generates (i attached the input with no restraints). The charges on the
individual residues are GLU (-1), ASP (-1), KCX (-1), MOH (-1), ZN1 (2+),
ZN2 (2+), and the rest are 0. The overall charge on the model is 0.
However, I would like the RESP charges on ZN and not the formal 2+ charge.
Regards,
Hashem
On 4/26/11 2:30 PM, "Ben Roberts" <ben.roberts.geek.nz> wrote:
>Hi Hashem,
>
>On 25/4/2011, at 1:49 p.m., Hashem Taha wrote:
>
>> does anyone have any ideas about the problem below?
>
>This seems a bit mysterious, which is probably why you haven't received
>any answers yet. Nevertheless, I'll try to assist.
>
>> On Thursday, April 21, 2011, Hashem Taha <htahaphd.gmail.com> wrote:
>>> Hi, I am trying to use MCPB for parameterization of a protein complex
>>>with two zinc ions. I have been following the tutorial included in the
>>>MTK++ manual. I am able to run all calculations without any problems.
>>>However, when I try to create the XML libraries containing the RESP
>>>charges, I run into some trouble. the overall charge on the model is 0
>>>(and this is what is used when doing the Gaussian charge calculations).
>>>
>>> problem: When I run "MCPB -i NAME_large_mk1.bcl", the generated .ac
>>>file has a charge of 1.32 and therefore 1 is used for the RESP
>>>calculations, and when I generate the final XML files including the new
>>>charges, the overall charge is -0.1557. I also attempted to manually
>>>edit the .ac file to change the charge to 0, and run the resp
>>>calculation again. However, this resulted in the same overall charge.
>>>This is true for all 4 resp methods (0, 1, 2, and 3).
>
>Can you send your RESP input file, if any?
>
>>> my large model (used for the charge calculations) has the following
>>>sequence, and the sidechain model (used for FC calculations) does not
>>>include the GLU residue that connects the two histidines or the capping
>>>residues (NME and ACE)
>>>
>>> ACE HID GLU HID NME ACE ASP NME ACE KCX NME ACE HID NME ACE HIE NME
>>>ZN1 ZN2 MOH HOH
>>>
>>> I'm assuming that the problem arises from how the charges of the
>>>capping residues (ACE NME) are handled, but I am not sure. any help
>>>would be appreciated.
>
>What are the charges on the various residues?
>
>Regards,
>Ben
>
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Received on Tue May 03 2011 - 09:00:03 PDT
