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
>>
>>
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>>
>
>
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Received on Tue Nov 01 2016 - 10:00:02 PDT
