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 &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
Thank you
Hi everyone,<
br>
I have one question about adding atoms that are missing in residue. This atom is OG in SER amino acid. I don't know how can I add this atom to my residue. If I have to add this atom manually how can I find coordinates of that? Or If there is server or software to do this I will be happy if you suggest me its.>
There's no automated GROMACS tool, and I haven't used any other particular tool
for the task. For just one atom + hydrogen, you're probably fine to guess
approximate coordinates and use EM to fix it.
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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