[gmx-users] pdb2gmx fails because of imaginary "Residue E"

[Justin Lemkul]

On 11/29/13 7:23 PM, kolnkempff wrote:
> pdb2gmx produces error message:
> Fatal error:
> Residue 'E' not found in residue topology database
>
> But there is no "Residue 'E' " in my pdb file (see below).  I have verified
> that all residues in the pdb file are listed in ffamber03.rtp and pdb2gmx
> does identify the ACE and NME caps.
>
>
> COMPND    UNNAMED
> AUTHOR    GENERATED BY OPEN BABEL 2.3.1
> ATOM    1  N   PHE     2       0.720   0.859  -0.499  1.00  0.00           N
> ATOM    2  C   PHE     2       0.760  -0.439   0.174  1.00  0.00           C
> ATOM    3  C   PHE     2       2.125  -1.161   0.111  1.00  0.00           C
> ATOM    4  O   PHE     2       2.253  -2.263   0.634  1.00  0.00           O
> ATOM    5  H   PHE     2       0.176   0.905  -1.352  1.00  0.00           H
> ATOM    6  H   PHE     2       0.585  -0.253   1.240  1.00  0.00           H
> ATOM    7  C   PHE     2      -0.336  -1.383  -0.373  1.00  0.00           C
> ATOM    8  C   PHE     2      -1.743  -0.858  -0.186  1.00  0.00           C
> ATOM    9  H   PHE     2      -0.200  -2.340   0.138  1.00  0.00           H
> ATOM   10  H   PHE     2      -0.145  -1.567  -1.440  1.00  0.00           H
> ATOM   11  C   PHE     2      -4.354   0.139   0.179  1.00  0.00           C
> ATOM   12  C   PHE     2      -2.316  -0.794   1.094  1.00  0.00           C
> ATOM   13  C   PHE     2      -2.504  -0.416  -1.277  1.00  0.00           C
> ATOM   14  C   PHE     2      -3.799   0.078  -1.100  1.00  0.00           C
> ATOM   15  C   PHE     2      -3.607  -0.301   1.276  1.00  0.00           C
> ATOM   16  H   PHE     2      -1.744  -1.138   1.954  1.00  0.00           H
> ATOM   17  H   PHE     2      -2.086  -0.476  -2.281  1.00  0.00           H
> ATOM   18  H   PHE     2      -4.373   0.412  -1.961  1.00  0.00           H
> ATOM   19  H   PHE     2      -4.033  -0.263   2.276  1.00  0.00           H
> ATOM   20  H   PHE     2      -5.362   0.519   0.320  1.00  0.00           H
> HETATM   21  C   ACE     1       0.873   2.036   0.208  1.00  0.00
> C

As you can see from this misalignment of columns, you have broken PDB format, 
hence residue 'E' is identified instead of the actual residue names.

-Justin

> HETATM   22  O   ACE     1       1.301   2.055   1.353  1.00  0.00
> O
> HETATM   23  C   ACE     1       0.484   3.302  -0.540  1.00  0.00
> C
> HETATM   24  H   ACE     1       1.253   4.060  -0.375  1.00  0.00
> H
> HETATM   25  H   ACE     1      -0.451   3.685  -0.116  1.00  0.00
> H
> HETATM   26  H   ACE     1       0.345   3.153  -1.616  1.00  0.00
> H
> HETATM   27  N   NME     3       3.115  -0.507  -0.549  1.00  0.00
> N
> HETATM   28  C   NME     3       4.474  -1.010  -0.616  1.00  0.00
> C
> HETATM   29  H   NME     3       5.163  -0.381  -0.040  1.00  0.00
> H
> HETATM   30  H   NME     3       4.474  -2.015  -0.195  1.00  0.00
> H
> HETATM   31  H   NME     3       4.822  -1.054  -1.654  1.00  0.00
> H
> HETATM   32  H   NME     3       2.906   0.422  -0.885  1.00  0.00
> H
> END
>
>
> --
> View this message in context: http://gromacs.5086.x6.nabble.com/pdb2gmx-fails-because-of-imaginary-Residue-E-tp5012928.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
>

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

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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