[gmx-users] first residue in chains warning issue

[Justin Lemkul]

On 5/10/15 11:36 PM, Ming Tang wrote:
> 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.
>

You'll need to provide the full screen output from pdb2gmx; this shouldn't 
happen if all the selections are made correctly and chain termini are identified 
as they should be.

> 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.
>

Because you're providing a fully protonated N-terminus (which is fine) with 
non-unique atom names (which pdb2gmx will take care of when using -ignh).

> 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.
>

You're using -ignh, so all H atoms are ignored per your instruction.

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

If the topology winds up being sane, then it's fine, but warnings from pdb2gmx 
are usually weird in the case of normal topologies.  Inspect the termini.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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