[gmx-users] pdb2gmx: Atom N used in the topology not found in the input (PDB) file

[Justin Lemkul]

On 5/19/17 5:37 PM, ZHANG Cheng wrote:
> Dear Gromacs,
> I got this fatal error after running "pdb2gmx":
>

Please provide your exact command and full screen output.  There's a lot of 
relevant information there, because pdb2gmx is doing a lot of complex things.

-Justin

>
> Fatal error:
> Residue 1 named ASP of a molecule in the input file was mapped
> to an entry in the topology database, but the atom N used in
> that entry is not found in the input file. Perhaps your atom
> and/or residue naming needs to be fixed.
>
>
>
> However, the residue 1 in the PDB is:
>
>
> ATOM      1  N   ASP L   1      24.330  14.711  -3.854  1.00  0.00           N
> ATOM      2  CA  ASP L   1      25.669  15.093  -3.310  1.00  0.00           C
> ATOM      3  C   ASP L   1      25.766  14.899  -1.791  1.00  0.00           C
> ATOM      4  O   ASP L   1      26.581  14.101  -1.318  1.00  0.00           O
> ATOM      5  CB  ASP L   1      25.989  16.552  -3.646  1.00  0.00           C
> ATOM      6  CG  ASP L   1      26.260  16.773  -5.128  1.00  0.00           C
> ATOM      7  OD1 ASP L   1      26.489  15.809  -5.821  1.00  0.00           O
> ATOM      8  OD2 ASP L   1      26.236  17.903  -5.554  1.00  0.00           O
> ATOM      9 1H   ASP L   1      24.318  14.855  -4.844  1.00  0.00           H
> ATOM     10 2H   ASP L   1      24.152  13.747  -3.656  1.00  0.00           H
> ATOM     11 3H   ASP L   1      23.623  15.275  -3.427  1.00  0.00           H
> ATOM     12  HA  ASP L   1      26.425  14.456  -3.771  1.00  0.00           H
> ATOM     13 1HB  ASP L   1      25.154  17.186  -3.346  1.00  0.00           H
> ATOM     14 2HB  ASP L   1      26.864  16.873  -3.080  1.00  0.00           H
>
>
>
> You can see that the first atom is just atom N, not missing. Can I ask why I still got this error?
>
>
> Another mutant file of the protein works totally fine for pdb2gmx. Its 1st residue ASP is the below, I could not see any big difference except slight difference in the coordinates.
>
>
> ATOM      1  N   ASP L   1      24.330  14.711  -3.854  1.00  0.00           N
> ATOM      2  CA  ASP L   1      25.669  15.093  -3.310  1.00  0.00           C
> ATOM      3  C   ASP L   1      25.766  14.899  -1.791  1.00  0.00           C
> ATOM      4  O   ASP L   1      26.586  14.106  -1.317  1.00  0.00           O
> ATOM      5  CB  ASP L   1      25.989  16.552  -3.646  1.00  0.00           C
> ATOM      6  CG  ASP L   1      26.260  16.773  -5.128  1.00  0.00           C
> ATOM      7  OD1 ASP L   1      26.489  15.810  -5.821  1.00  0.00           O
> ATOM      8  OD2 ASP L   1      26.235  17.904  -5.554  1.00  0.00           O
> ATOM      9 1H   ASP L   1      24.318  14.855  -4.844  1.00  0.00           H
> ATOM     10 2H   ASP L   1      24.152  13.747  -3.656  1.00  0.00           H
> ATOM     11 3H   ASP L   1      23.623  15.275  -3.427  1.00  0.00           H
> ATOM     12  HA  ASP L   1      26.425  14.456  -3.771  1.00  0.00           H
> ATOM     13 1HB  ASP L   1      25.154  17.186  -3.345  1.00  0.00           H
> ATOM     14 2HB  ASP L   1      26.864  16.872  -3.080  1.00  0.00           H
>
>
> Thank you.
>
>
> Yours sincerely
> Cheng
>

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

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

==================================================