There was discussion at the AMBER developers meeting to standardize the order
so that the A B and D atoms are sorted on a key made from the atom type followed by the atom name.
This is the sorting scheme that I will use in CANDO. It will be backwards compatible and provide consistency.
Christian Schafmeister
Professor
Chemistry Department
Temple University
meister.temple.edu
> On Mar 24, 2016, at 2:02 AM, David Cerutti <dscerutti.gmail.com> wrote:
>
> OK, good to know the history. Thanks Bill!
>
> On Thu, Mar 24, 2016 at 2:01 AM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>
>>> 1.) Can anyone tell me a little more about the origins of this
>> convention, or at least assure me that I'm doing the right thing in
>> enforcing it?
>>
>> We had to come up with a convention when we switched from explicitly
>> defined, residue-based impropers to topologically-applied parameters, and
>> Peter Kollman made the final call on the convention. I believe I raised the
>> issue, since it arose in the work on leap and validating the new code
>> against the old. You are doing the right thing in enforcing it in that
>> consistency seems valuable.
>>
>> Note that this form doesn't work for nonplanar impropers because placement
>> is ambiguous when there are duplicate atom types. We decided to kick this
>> problem down the road.
>>
>>
>>> 2.) Can anyone confirm that, for any atom types A, B, and D, an
>> improper A B C D is equivalent to an improper D B C A and also B D C A,
>> or any other permutation that leaves C in position 3?
>>
>> I suspect the forces on the atoms in a given conformation might be
>> different with different ordering of the terms, but the goal of
>> enforcing planarity over time would be achieved either way.
>>
>> Bill
>>
>>
>> On 3/23/16 10:42 PM, David Cerutti wrote:
>>> I'm posing this to the reflector in the hopes of a faster response. I've
>>> had a student come to me with a parameterization question, and I'd like
>> to
>>> help him, but mdgx is choking when it cannot find an improper torsion
>> with
>>> the ingredients "c3 na ca ca." Nonsense, I said, this is right
>> there
>>> in the gaff.dat file we're referencing. However, the problem seems to be
>>> that the improper is "ca-ca-na-c3" because of the naming conventions for
>>> impropers. It seems that for an improper dihedral with atom types A, B,
>> C,
>>> D, the third atom type is the central atom, and that the first, second,
>> and
>>> fourth atom types should then be given in alphabetical order. I even
>> have
>>> a function, from years ago when I was writing this section of mdgx, which
>>> enforces the alphabetical ordering of impropers.
>>>
>>> 1.) Can anyone tell me a little more about the origins of this
>> convention,
>>> or at least assure me that I'm doing the right thing in enforcing it?
>>>
>>> 2.) Can anyone confirm that, for any atom types A, B, and D, an improper
>> A
>>> B C D is equivalent to an improper D B C A and also B D C A, or any other
>>> permutation that leaves C in position 3?
>>>
>>> Thanks!
>>>
>>> Dave
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>>
>>
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Received on Wed Mar 23 2016 - 23:30:05 PDT
