[gmx-users] add missing atoms

[Justin A. Lemkul]

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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-- 
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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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