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

From: Eric Pettersen <>
Date: Tue, 31 Mar 2009 18:51:22 +0100

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.


AMBER-Developers mailing list
Received on Wed Apr 01 2009 - 01:16:26 PDT
Custom Search