From: David A. Case <>
Date: Wed, 28 Mar 2012 15:25:45 -0400

On Wed, Mar 28, 2012, Olena Dobrovolska wrote:

> But as you can see there in Final results part there are CB, CG atoms,
> whereas, there should be protons, as it is in dist file. I checked my
> RST file and found that there is a problem: sometimes the atom number
> doesn't correspond to the atom name, for example,
> # 30 LEU QQD 85 VAL QQG 4.38 (#peak 1066)

You misunderstand what makeDIST_RST is doing. If you use highly averaged
pseudoatoms like "QQD" or "QQG", it maps them onto the apprpriate carbon
atoms. (I think that CYANA/DIANA does the same, but I'm not sure.) If you
want a different mapping, you need to change the map file that defines what
things like "QQD" mean.

> &rst
> ixpk= 1066, nxpk= 0, iat= 74, 967, r1= 1.30, r2= 1.80, r3= 4.38, r4= 4.88, &end
> #
> but in my pdb file 967 number has CB atom of VAl 85. And this mess is
> not regular, so I can't figure why it creates RST file in such way.

This is exactly what you should be expecting, and I don't think it is in fact
a "mess". There are other ways to treat valine methyl protons that are not
stereospecifically assigned, but the way Amber does it has a very long
history. Note also that these are conservative restraints: if your structure
is violating these restraints, you would be seeing violations as well for any
other reasonable way of using such NOE peaks.

As I suggested before, examine one-by-one the restraints that have the biggest
violations, and see if there might be some problems in your input files. I
don't see any evidence here for problems with the codes.


AMBER mailing list
Received on Wed Mar 28 2012 - 12:30:05 PDT
Custom Search