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

From: Eric Pettersen <>
Date: Tue, 31 Mar 2009 19:35:15 +0100

On Mar 31, 2009, at 11:28 AM, Joe Krahn wrote:

>> 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.)

Well, yes, the rules are still the same as v2 except for 4-character
atom names. And those rules always were that the atomic symbol is
right justified in columns 13-14 and the remainder of the atom name is
left justified in columns 15-16. Obviously, 4-character hydrogen
names were a problem in that scheme. The v2 behavior was to rotate
the last character of the name into column 13. The v3 behavior is to
put that name as is into columns 13-16.


AMBER-Developers mailing list
Received on Wed Apr 01 2009 - 01:16:44 PDT
Custom Search