I agree with Ross. Adding new sections would be better than make
changes to current format.
On Mar 7, 2009, at 2:30 PM, "Ross Walker" <ross.rosswalker.co.uk> wrote:
>> I just had a simple idea about avoiding residue-number versus
>> residue-index conflicts. There can be a flag to enable the new
>> residue
>> number syntax, which can initially default to off, and eventually
>> default to on. When enabled, the residue index could still be
>> available
>> with a syntax like "#123".
>>
>> I will go ahead and implement something, because it will make things
>> easier for comparing SANDER output with crystal structures.
>
> I don't understand why it needs to be this complicated. Why not just
> include
> both sections in the prmtop file. The key is that it needs a comment
> about
> the fact that sander and pmemd don't use that data and just ignore
> it. The
> real advantage is for visualization programs which will all need to be
> updated to read this info so they can display it within the program.
> Thus we
> need to define a very clear and concise standard for including this
> in the
> prmtop file so we can tell people like John Stone (VMD) what they
> need to
> read.
>
> Additionally remember that many programs read amber prmtop files -
> don't
> forget that you will need to update ambpdb as well as ptraj and a
> bunch of
> other codes to make sure they read this data.
>
> I would avoid the issue of having some kind of flag in there that is
> initially off and then later turned on since I think this will just
> make the
> code more confusing and I suspect that down the road the purpose of
> this
> flag will ultimately get lost and then people won't be able to
> follow what
> is going on or why it is there. Why not just have two sections
> similar to
> the following (with more detailed comments of course):
>
> %FLAG RESIDUE_INDEX
> %COMMENT The residue indexes as generated by Leap
> %FORMAT(10i8)
> 1 2 1 ......
>
> %FLAG RESIDUE_NUMBER
> %COMMENT The residue number as read from the pdb file
> %FORMAT (10i8)
> 1 2 3 .......
>
> These sections can go immediately after the RESIDUE_LABEL flag in
> the prmtop
> file. Remember though that if you update the prmtop file you need to
> test
> EVERYTHING including third party applications that are commonly used
> (VMD,
> Sirius, Chimera, ...) including both current and previous versions
> (probably
> back to at least AMBER 8 in amber) and then put together any necessary
> patches and/or contact the third party software authors and explain
> what has
> changed and ask them to update their codes.
>
> All the best
> Ross
>
>
> /\
> \/
> |\oss Walker
>
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> | http://www.rosswalker.co.uk | PGP Key available on request |
>
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>
>
>
>
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Received on Sun Mar 08 2009 - 01:21:20 PST
