[gmx-users] first residue in chains warning issue

[Ming Tang]

Dear all,

I built a triple helix with 2 GLN and 1 SER being the first residue of the three chains. However, while using pdb2gmx -f 1.pdb -o complex.gro -ignh -ter -ff gromos54a7 -water SPC and choosing NH2 or NH3+ as the start terminus type for GLN-1  and SER-1, I came across the following warnings:

WARNING: WARNING: Residue 1 named GLN (SER) of a molecule in the input file was mapped to an entry in the topology database, but the atom H used in
an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed.

Then, I checked the .pdb and .rtp files. The difference between GLN-1/SER-1 and GLN-n/SER-n (n>1) is that GLN-1/SER-1 contains 2 more H atoms.

Residue GLN-1 in .pdb
ATOM      1  N   GLN A   1     -10.554  16.421  -0.030  1.00  0.00           N1+
ATOM      2  CA  GLN A   1     -10.080  16.667   1.238  1.00  0.00           C
ATOM      3  C   GLN A   1      -9.305  15.495   1.835  1.00  0.00           C
ATOM      4  O   GLN A   1      -9.636  14.335   1.608  1.00  0.00           O
ATOM      5  CB  GLN A   1     -11.222  17.053   2.210  1.00  0.00           C
ATOM      6  CD  GLN A   1     -11.943  17.895   4.480  1.00  0.00           C
ATOM      7  NE2 GLN A   1     -11.643  18.268   5.719  1.00  0.00           N
ATOM      8  OE1 GLN A   1     -13.093  17.905   4.041  1.00  0.00           O
ATOM      9  CG  GLN A   1     -10.784  17.445   3.612  1.00  0.00           C
ATOM     10  HE2 GLN A   1     -12.366  18.573   6.339  1.00  0.00           H
ATOM     11  HE2 GLN A   1     -10.694  18.243   6.032  1.00  0.00           H
ATOM     12  H   GLN A   1     -11.086  17.245  -0.422  1.00  0.00           H
ATOM     13  H   GLN A   1      -9.773  16.207  -0.708  1.00  0.00           H
ATOM     14  H   GLN A   1     -11.212  15.593  -0.048  1.00  0.00           H

Parameters in .rtp in gromos54a7
[ GLN ]
[ atoms ]
    N     N    -0.31000     0
    H     H     0.31000     0
   CA   CH1     0.00000     1
   CB   CH2     0.00000     1
   CG   CH2     0.00000     1
   CD     C     0.29000     2
 OE1     O    -0.45000     2
  NE2    NT    -0.72000     2
HE21     H     0.44000     2
HE22     H     0.44000     2
    C     C       0.450     3
    O     O      -0.450     3
[ angles ]
;  ai    aj    ak   gromos type
   -C     N     H     ga_32
   -C     N    CA     ga_31
    H     N    CA     ga_18
    N    CA    CB     ga_13
    N    CA     C     ga_13
   CB    CA     C     ga_13
   CA    CB    CG     ga_15
   CB    CG    CD     ga_15
   CG    CD   OE1     ga_30
   CG    CD   NE2     ga_19
  OE1    CD   NE2     ga_33
   CD   NE2  HE21     ga_23
   CD   NE2  HE22     ga_23
 HE21   NE2  HE22     ga_24
   CA     C     O     ga_30
   CA     C    +N     ga_19
O     C    +N     ga_33

Further, I compared atoms of GLN in .pdb and .rtp, and changed 2 HE into HE21 and HE22, but got the same warnings.

The simulation can be move forward to EM and NPT smoothly. Does this kind of warning affect the simulation results significantly?

Thanks in advance.