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

From: Joe Krahn <>
Date: Tue, 31 Mar 2009 19:28:34 +0100

Eric Pettersen wrote:
> On Mar 31, 2009, at 10:27 AM, Joe Krahn wrote:
>> 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 know if this is of any help, but Chimera uses the v2 alignment
> except for 4-character atom names (typically hydrogens) which simply
> get stuffed into the 4 available columns without the old v2 rotate-
> last-character-into-first-column behavior. I believe this results in
> v3 names in all cases.
> --Eric
That is true for protein and nucleic acid, but not heterogens. For
example, chloride "CL" is still left-justified. In general, heterogens
follow the old system. But, non-standard amino acids are also
heterogens. (Chimera developers are one of the groups who complained
about the new alignment rules, to no avail.)


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Received on Wed Apr 01 2009 - 01:16:42 PDT
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