From: faride badalkhani (farideh.khamseh_at_gmail.com)
Date: Fri Mar 18 2016 - 13:36:14 CDT
Dear Josh,
I have run my structure through CGenFF and got the parameters and charges.
According to this file
Penalties lower than 10 indicate the analogy is fair; penalties between 10
and 50 mean some basic validation is recommended; penalties higher than 50
indicate poor analogy and mandate extensive validation/optimization.
The penalties in the .str file of my structure are not higher than 50, but
there are some penalties between 10 and 50.
Could you tell me what does basic validation mean? What kind of
optimizations or calculations should I perform?
Truly yours,
Farideh
On Fri, Mar 18, 2016 at 8:18 PM, faride badalkhani <
farideh.khamseh_at_gmail.com> wrote:
> Thanks a lot for your answer.
>
> Regards,
> Farideh
>
> On Fri, Mar 18, 2016 at 8:06 PM, Josh Vermaas <vermaas2_at_illinois.edu>
> wrote:
>
>> There isn't a hard rule. For CHARMM, the first thing I'd do is run your
>> structure through CGenFF. Are the penalties high? If they aren't,
>> parameterization by analogy is defensible (probably), and due to its
>> expediency, its hard to argue against. If the penalties are high, you get
>> to parameterize it yourself. Which is hard. Hard enough that it will suck
>> up at least a month of your time and you still won't be sure if its
>> "right", because parameterization is *HARD*, and there is alot to learn.
>>
>> -Josh
>>
>>
>> On 03/18/2016 11:23 AM, faride badalkhani wrote:
>>
>> Thanks a lot dear Josh. I want to simulate a hyperbranched polymer and I
>> have some problem with charge assignment. which one do you recommend:
>> 1) performing ab initio calculations to find atomic charges or
>> 2) using the atomic charges near to my structure from CHARMM 36 topology
>> file (I am using this FF)?
>>
>> Truly yours,
>> Farideh
>>
>> On Fri, Mar 18, 2016 at 7:40 PM, Josh Vermaas <vermaas2_at_illinois.edu>
>> wrote:
>>
>>> Hi Farideh,
>>>
>>> Charge groups should be integers, and used to be mandatory before PME
>>> took care of long range electrostatics, since they were used to make sure
>>> that a dipole didn't get split across a cutoff-boundary. Now they are just
>>> nice to have, but I don't believe they are mandatory.
>>>
>>> -Josh Vermaas
>>>
>>>
>>> On 03/18/2016 10:56 AM, faride badalkhani wrote:
>>>
>>> Dear all,
>>>
>>> I need to know if it is mandatory to define charge groups in residues?
>>> and if it is, should total charge of each charge group be equal to zero?
>>>
>>> any help will be appreciated.
>>>
>>> Truly yours,
>>> Farideh
>>>
>>>
>>>
>>
>>
>
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