AMBER Archive (2005)

Subject: Re: AMBER: parm99.dat non-bonded parameters

From: Anthony Fejes (fejes_at_zymeworks.com)
Date: Fri Aug 19 2005 - 13:18:36 CDT

Angela,

I'm not the right person to answer this, from a code perspective.
However, I am unaware of any mechanism for checking for redundancy or
self-consistency in the parm files, short of errors given while they are
being used.

In this case, it doesn't much matter, as the NY line is set equivalent
to N, and has it's own line where NY is also given values equivalent to N.

I would suggest that the NY line in the 6-12 section be removed for clarity.

I would be curious to know, however, what the outcome would be if the NY
line in the 12-6 section were modified. I believe, from what I've read
elsewhere, that AMBER programs would use the first occurrence that they
find, when searching the tables.

My *guess* would be that NY set equal to N in the equivalence line would
be found first, and would ignore any changes on the changed 6-12 NY
line. If anyone has the time and inclination, they *should* have to
look at the code to be sure which line is processed first, or if I am
incorrect about the lack of redundancy checking between the equivalence
line and the 6-12 section.

Anthony Fejes

Angela Liu wrote:
> Dear Anthony,
>
> Thanks a lot! I missed that file while visiting the
> formats website.
> But that would mean that the NY line in the nonbon
> section should not be there (parm99.dat) because the
> NY is set to be equivalent to N, right? (Their R and
> E are the same, so it didn't matter.)
>
> Thank you again for taking your time to help!
>
> Best wishes,
> Angela
>
> --- Anthony Fejes <fejes_at_zymeworks.com> wrote:
>
>
>>A good reference for questions like this is the
>>Amber file format
>>specifications:
>>
>>http://amber.scripps.edu/formats.html
>>
>>In the section on Force field parameter file
>>specifications, section 9
>>is "INPUT FOR EQUIVALENCING ATOM SYMBOLS FOR THE
>>NON-BONDED 6-12
>>POTENTIAL PARAMETERS".
>>
>>The corresponding lines in parm99.dat are:
>>
>>N NA N2 N* NC NB NT NP NO NY
>>C* CA CB CC CD CK CM CN CQ CR CV CW CX
>>CY CZ
>>
>>These are used to set all of the Nitrogens that are
>>not explicitly
>>mentioned otherwise in the 6-12 parameter section as
>>equal to the type
>>N, and likewise, all of the C types that are not
>>otherwise mentioned as C*.
>>
>>I hope that helps,
>>
>>Anthony Fejes
>>
>>
>>
>>Angela Liu wrote:
>>
>>>Dear Amber developers and users,
>>>
>>>In the Amber parameter files such as parm99.dat
>>>($AMBERHOME/dat/leap/parm/), not all atom types
>>
>>have
>>
>>>their non-bonded parameters defined. For
>>
>>instance,
>>
>>>only N, N3, and NY show defined R (radius) and E
>>
>>(well
>>
>>>depth) values among all the nitrogen atom types.
>>>Other nitrogen types, NA, NB, NC, N2, N#, NT, and
>>
>>N*,
>>
>>>do not appear in the non-bonded section.
>>>
>>>My questions are:
>>>1) Is it LEaP that assigns the non-bonded
>>
>>parameters
>>
>>>for these atom types?
>>>2) Is the assignment based on the hybridization
>>
>>states
>>
>>>and the element number?
>>>
>>>Thanks a lot for your time and help!
>>>
>>>Angela
>>>
>>>__________________________________________________
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>>
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>
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-- 
Anthony Fejes
Chief Scientific Officer
Zymeworks Inc. - A Catalyst in Design

201-1401 West Broadway Ave,
Vancouver, B.C.
Canada, V6H 1H6

www.zymeworks.com
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