[gmx-users] Re: add missing atom(s)

[chris.neale at utoronto.ca]

I use a program called Loopy to build in missing backbone atoms and a  
program called SCWRL3 to add in missing sidechains. I'm not advocating  
these as better than other methods, just that they work for me. You'll  
need to do some reading for each though in order to be sure that you  
do it correctly -- it is entirely possible to have an automated atom  
placement routing do something really silly and obviously incorrect so  
be sure to visualize everything.

Chris.

-- original message --

you zou wrote:
Hi again,

Sorry, in "REMARK 470" there is:

REMARK 470

REMARK 470 MISSING ATOM

REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;

REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;

REMARK 470 I=INSERTION CODE):

REMARK 470 M RES CSSEQI ATOMS

REMARK 470 SER A 2 OG

REMARK 470 GLN A 678 CA C O &a
   mp;nbs
p; CB CG CD OE1 NE2

REMARK 470 SER B 2 OG

REMARK 470 GLY B 679 CA C O

This means there are missing atoms. Is it possible to add these atoms
from other residue what are SER and GLN and GLY?( Copy and Paste OG from
other SER for example?) I think after EM these are fixed, it is true?
If you have several missing atoms you will have to use some external  
tool(s) to
re-create these residues. Using cute tricks to build back one atom is easy
enough, but re-creating a fragmented structure is much easier using tools
designed for the task.

-Justin