[gmx-users] Warning: atom is missing in residue

[Ehsan Sadeghi]

Hi gmx users,

When I run gromacs, there is an issue with the molecules with more than one residue. for example, for this pdb file:

ATOM      1  C1  VOD     0       8.441   1.158   0.141  1.00  0.00           C  
ATOM      2  H1  VOD     0       9.420   1.340   0.570  1.00  0.00           H  
ATOM      3  H2  VOD     0       8.580   0.090   0.040  1.00  0.00           H  
ATOM      4  H3  VOD     0       8.696   0.757  -0.666  1.00  0.00           H  
ATOM      5  C2  VOD     1       7.270   1.800   0.740  1.00  0.00           C  
ATOM      6  H4  VOD     1       6.440   1.830   0.030  1.00  0.00           H  
ATOM      7  H5  VOD     1       6.950   1.150   1.550  1.00  0.00           H  
ATOM      8  O   VOD     1       7.640   3.100   1.130  1.00  0.00           O  
ATOM      9  H6  VOD     1       8.300   3.360   0.500  1.00  0.00           H  

The corresponding residue in aminoacids.rtp is:

[ VOD ]
 [ atoms ]
   C1  CH2    -0.18000     0
   H1    H     0.06000     0
   H2    H     0.06000     0
   H3    H     0.06000     0
   C2  CH3     0.14500     1
   H4    H     0.06000     1
   H5    H     0.06000     1
    O   OA    -0.68300     1
   H6    H     0.41800     1     
 [ bonds ]
   C1   H1    gb_2
   C1   H2    gb_2
   C1   H3    gb_2
   C1   C2    gb_27
   C2   H4    gb_2
   C2   H5    gb_2
   C2   O     gb_18
    O   H6    gb_1
 [ angles ]
;  ai    aj    ak   gromos type
    H1    C1    H2     ga_19 
    H1    C1    H3     ga_19 
    H1    C1    C2     ga_19 
    H2    C1    H3     ga_19 
    H2    C1    C2     ga_19
    H3    C1    C2     ga_19 
    C1    C2    H4     ga_19 
    C1    C2    H5     ga_19 
    C1    C2     O     ga_13 
    H4    C2    H5     ga_19 
    H4    C2     O     ga_30
    H5    C2     O     ga_30 
    C2     O    H6     ga_30 

Problem: When I use pdb2gmx here are the warnings:

-----------------------------------

WARNING: atom C2 is missing in residue VOD 0 in the pdb file


WARNING: atom H4 is missing in residue VOD 0 in the pdb file
         


WARNING: atom H5 is missing in residue VOD 0 in the pdb file


WARNING: atom O is missing in residue VOD 0 in the pdb file


WARNING: atom H6 is missing in residue VOD 0 in the pdb file
-----------------------

When I combine these 2 residues and make it one, there is no warning. Does anybody know what is the problem?

Regards,
Ehsan