Re: [AMBER-Developers] new CVS versions of leaprc.ff99bsc0 and ambpdb.f

From: David A. Case <>
Date: Tue, 31 Mar 2009 21:46:51 +0100

On Tue, Mar 31, 2009, Joe Krahn wrote:

> My own solution is to have PDB name conversion tables in a data file.
> The file can hold any number of naming variations, and makes it easy to
> convert among any defined variation. It can also be modified without
> recompiling anything.

This sounds a lot like the PdbAtomMap and PdbResMap tables in leap. We
can/should make version2 and version3 variants of these, to make it
easier for people to use either type of file.

> Using CNS, I created my own set of topology files that use PDB version 3
> nomenclature. It makes things a lot easier. However, it is not a perfect
> solution. PDB v3 has a very badly designed atom name alignment.
> Sometime, it follows PDB v2 element-alignment, but other times it does
> not. The only way to get it right is to either keep the leading space in
> tact everywhere, or to add an additional alignment flag data item. Since
> Leap is too inflexible, it will still probably require a data table.

I don't see that the leading space in v3 is much of a problem,
myself. And what they have is better than v2. I'm not quite sure what
inflexibility in LEaP you are referring to, but Wei seems willing to put
almost any beahvior into sleap, so you should make your needs known.


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Received on Wed Apr 01 2009 - 01:17:30 PDT
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