Let me correct my previous email. Apparently, I do not have SCF convergence
problems (QCSCF skips out because SCF is already converged). But the
calculation still ends with "Error termination via Lnk1e in
/softwares/g09/l602.exe". Log file still contains ESP sections, but no
other errors.
Is that right?
Fabrício
2016-06-29 13:32 GMT-03:00 Fabrício Bracht <fabracht1.gmail.com>:
> Hi Pengfei.
> I have a question regarding the gaussian calculation of the large model.
> From the input file, I can see that no geometry optimization is performed
> on this model. I encountered convergence problems with this step. I am
> guessing that, since the geometry of the complex obtained directly from the
> pdb is not that great, the SCF routine has problems with convergence (hence
> the XQC flag). Is that correct?
> But even so, the large model gaussian calculation terminates with an error.
> Is there something else I could do to fix this?
>
> Thanks
> Fabrício
>
> 2016-06-28 11:33 GMT-03:00 Pengfei Li <ambermailpengfei.gmail.com>:
>
>> Hi Fabricio,
>>
>> I have modified MCPB.py code to make it can work for your case. And I
>> have sent an email to your email address about that. Hope it helps.
>>
>> Kind regards,
>> Pengfei
>>
>> > On Jun 27, 2016, at 3:56 PM, Fabrício Bracht <fabracht1.gmail.com>
>> wrote:
>> >
>> > Hello. I've given up on using MCPB.py, and am trying to use MCPB
>> instead.
>> > I need to create a Histidine residue that has a methyl group bonded to
>> the
>> > epsilon nitrogen instead of the hydrogen that would be there.
>> > So far I've tried to introduce a terminal CH3 with the command:
>> >
>> > addFragment terminal/CH3 bd /NAME/CLR/HD1-1/.NE2 ag
>> /NAME/CLR/HD1-1/.CD2 tr
>> > /NAME/CLR/HD1-1/.CE1 165.00
>> >
>> > This works fine, but the HE2 is still there. There is no command listed
>> on
>> > the manual to remove atoms. I could, change the HIE to a HID and
>> transfer
>> > the hydrogen to the other nitrogen atom, but the other nitrogen is
>> bonded
>> > to the metal ion.
>> > Can I replace atoms or even remove them in MCPB?
>> >
>> > Thank you
>> > Fabrício
>> > _______________________________________________
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>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
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>
>
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Received on Wed Jun 29 2016 - 10:00:04 PDT
