[gmx-users] add missing atoms

you zou zou.you at live.com
Tue Jun 1 00:22:36 CEST 2010

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    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?
Thank you
> Hi everyone,

> 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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