Hi Fabricio,
You may have different mol2 files from previous for modeling, which caused the problem. You can send me the modeling files (MCPB.py input file, relevant PDB and mol2 files as well as the Gaussian output fchk file for the small model and log file for the large model) in an separate email. I can help to do a check.
Kind regards,
Pengfei
> On Nov 1, 2016, at 11:49 AM, Fabrício Bracht <fabracht1.gmail.com> wrote:
>
> But now there is another problem. There is a histidine residue which has
> both the backbone nitrogen and delta nitrogen bound to the copper atom.
> These atoms are renamed Y1 and Y2. They were not included in the final
> frcmod file. This has happened also for the model I was redoing, which
> worked fine the first time I did a couple of months ago.
> Fabrício
>
> 2016-11-01 14:28 GMT-02:00 Fabrício Bracht <fabracht1.gmail.com>:
>
>> Hi Pengfei
>> It worked for all models.
>> Thanks
>> Fabrício
>>
>> 2016-11-01 14:16 GMT-02:00 Pengfei Li <ambermailpengfei.gmail.com>:
>>
>>> Hi Fabrico,
>>>
>>> The problem could be about the wrong total charge during the RESP charge
>>> fitting.
>>>
>>> Which means when MCPB.py calculate the total charge by itself it adds up
>>> the partial charges in the database and mol2 files you created. This may be
>>> different from the actual charge of the system.
>>>
>>> The quick way to solve this problem is to add “lgmodel_chg" keyword to
>>> define the large model total charge by yourself and then perform the third
>>> step modeling of MCPB.py again.
>>>
>>> Please let me know whether it works.
>>>
>>> Kind regards,
>>> Pengfei
>>>
>>>> On Nov 1, 2016, at 9:58 AM, Fabrício Bracht <fabracht1.gmail.com>
>>> wrote:
>>>>
>>>> Hi Pengfei. I recently had to redo a parameterization in order to get
>>> the
>>>> original mol2 files. I had to do this because my computer was stolen
>>> and on
>>>> the cluster I only had the topology files.
>>>> Although I used the exact same files, now I get charges that are
>>> sometimes
>>>> very different. For example charges of 2.84 on a CT atom and -1.95 on a
>>> CR
>>>> atom.
>>>> I have encountered a similar problem while trying to parameterize a new
>>>> system which included a ligand. First I thought it was something
>>> related to
>>>> the gaussian calculation, but when the same thing happened to the
>>> system I
>>>> had already worked on, I figured something might be off.
>>>> I am using the release2 version of MCPB.py because it seems to be the
>>> only
>>>> one that recognizes a N terminal histidine as NHIC (which is one of the
>>>> residues that binds to the metal atom).
>>>>
>>>> Any ideas?
>>>> Thanks
>>>> Fabrício
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Nov 02 2016 - 19:30:03 PDT
