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 Apr 26 2011 - 12:00:03 PDT
