Firstly, thank you very much for your time and expertise, Jason and
Hannes. We all have much to do, and appreciate your emails.
Jason, I just attempted to use parmchk2 (I did not know of the command
before your email). I have a very vague sense of what's going on using
this command from the manual. Can you give me some guidance as to where
I might understand more about the scoring? For example, I produce
penalty scores for dihedrals of 232 and an improper dihedral of 41.2...I
have absolutely no sense on what this indicates on parameter quality. A
quick google search just brought up questions of segmentation faults
associated with it.
In my incredible ignorance of force fields, I would think the parameter
for dihedrals of such a planar aromatic molecule are going to be
similar? That they will all be equally un-floppy?
On 4/28/15 9:56 AM, Jason Swails wrote:
> On Tue, Apr 28, 2015 at 9:51 AM, Robert Molt <rwmolt07.gmail.com> wrote:
>
>> Hello,
>>
>> The definitions of the terms may be an issue here, for me. You describe
>> cc as "non-pure aromatic system." I do not know what that means? In the
>> original GAFF paper, it describes it as "inner sp2 carbon on conjugated
>> ring systems." I assume that means the fusion points (the "inner" part)
>> on these conjugated rings, and hence there have to be exactly two.
>>
>> Regardless, if the system is sufficiently non-canonical that either
>>
>> a.) antechamber's specific atom designation subroutine called makes a
>> "mistake" in designation
>> b.) antechamber's specific atom designation subroutine does NOT make a
>> mistake and parameters are missing
>>
>> then I should perhaps parameterize this on my own.
>>
> Did you by any chance try to use parmchk2 to "fill-in" the missing
> parameters? If not, there's a good chance that parmchk2 will be able to
> find some suitable parameters for you.
>
> Also, purine is a rather common biological fragment, so I doubt it lies
> outside of the chemical space targeted by antechamber.
>
> All the best,
> Jason
>
--
Dr. Robert Molt Jr.
r.molt.chemical.physics.gmail.com
Nigel Richards Research Group
Department of Chemistry & Chemical Biology
Indiana University-Purdue University Indianapolis
LD 326
402 N. Blackford St.
Indianapolis, IN 46202
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Received on Tue Apr 28 2015 - 18:00:03 PDT
