[gmx-users] question

[Justin Lemkul]

On 5/20/15 3:21 AM, Andrew Bostick wrote:
> Dear Justin
>
> I was really confused. I know that my peroblem is in incorrect entries
> (LYS2 and GLU2) in aminoacids.rtp file
>
> Sinse I want to have a isopeptide bond between (CD atom of GLU residue
> from chain B and NZ atom of LYS residue from chain E), thus I should
> use one HZ atom (for LYS2) and one OE atom (for GLU2) as follows. Is my
> vision true?
>
> [ GLU2 ]
>   [ atoms ]
>      N     N    -0.28000     0
>      H     H     0.28000     0
>     CA   CH1     0.00000     1
>     CB   CH2     0.00000     1
>     CG   CH2     0.00000     1
>     CD     C     0.50000     2
>     OE    OM    -0.50000     2
>      C     C       0.380     3
>      O     O      -0.380     3
>   [ bonds ]
>      N     H    gb_2
>      N    CA    gb_20
>     CA     C    gb_26
>      C     O    gb_4
>      C    +N    gb_9
>     CA    CB    gb_26
>     CB    CG    gb_26
>     CG    CD    gb_26
>     CD    OE    gb_5
>   [ angles ]
> ;  ai    aj    ak   gromos type
>     -C     N     H     ga_31
>      H     N    CA     ga_17
>     -C     N    CA     ga_30
>      N    CA     C     ga_12
>     CA     C    +N     ga_18
>     CA     C     O     ga_29
>      O     C    +N     ga_32
>      N    CA    CB     ga_12
>      C    CA    CB     ga_12
>     CA    CB    CG     ga_14
>     CB    CG    CD     ga_14
>     CG    CD    OE     ga_21
>   [ impropers ]
> ;  ai    aj    ak    al   gromos type
>      N    -C    CA     H     gi_1
>      C    CA    +N     O     gi_1
>     CA     N     C    CB     gi_2
>   [ dihedrals ]
> ;  ai    aj    ak    al   gromos type
>    -CA    -C     N    CA     gd_4
>     -C     N    CA     C     gd_19
>      N    CA     C    +N     gd_20
>      N    CA    CB    CG     gd_17
>     CA    CB    CG    CD     gd_17
>
>
> [ LYS2 ]
>   [ atoms ]
>      N     N    -0.28000     0
>      H     H     0.28000     0
>     CA   CH1     0.00000     1
>     CB   CH2     0.00000     1
>     CG   CH2     0.00000     2
>     CD   CH2     0.00000     2
>     CE   CH2     0.00000     3
>     NZ    NT    -0.50000     3
>     HZ     H     0.50000     3
>      C     C       0.380     4
>      O     O      -0.380     4
>   [ bonds ]
>      N     H    gb_2
>      N    CA    gb_20
>     CA     C    gb_26
>      C     O    gb_4
>      C    +N    gb_9
>     CA    CB    gb_26
>     CB    CG    gb_26
>     CG    CD    gb_26
>     CD    CE    gb_26
>     CE    NZ    gb_20
>     NZ    HZ    gb_2
>   [ angles ]
> ;  ai    aj    ak   gromos type
>     -C     N     H     ga_31
>      H     N    CA     ga_17
>     -C     N    CA     ga_30
>      N    CA     C     ga_12
>     CA     C    +N     ga_18
>     CA     C     O     ga_29
>      O     C    +N     ga_32
>      N    CA    CB     ga_12
>      C    CA    CB     ga_12
>     CA    CB    CG     ga_14
>     CB    CG    CD     ga_14
>     CG    CD    CE     ga_14
>     CD    CE    NZ     ga_14
>     CE    NZ    HZ     ga_10
>   [ impropers ]
> ;  ai    aj    ak    al   gromos type
>      N    -C    CA     H     gi_1
>      C    CA    +N     O     gi_1
>     CA     N     C    CB     gi_2
>   [ dihedrals ]
> ;  ai    aj    ak    al   gromos type
>    -CA    -C     N    CA     gd_4
>     -C     N    CA     C     gd_19
>      N    CA     C    +N     gd_20
>      N    CA    CB    CG     gd_17
>     CA    CB    CG    CD     gd_17
>     CB    CG    CD    CE     gd_17
>     CG    CD    CE    NZ     gd_17
>     CD    CE    NZ    HZ     gd_14
> ----------------------------------------------------------------------------
> Unfortunately, after using pdb2gmx, I encountered with:
>
> Linking CYS-252 SG-248 and CYS-312 SG-743...
> Linking CYS-358 SG-1094 and CYS-416 SG-1565...
> Linking GLU-380 CD-1269 and LYS-540 NZ-2499...
> Start terminus PRO-220: PRO-NH2+
> End terminus HIS-434: COO-
> Start terminus GLY-435: GLY-NH3+
> End terminus LYS-551: COO-
>
> -------------------------------------------------------
> Program gmx, VERSION 5.0.5
> Source code file:
> /export/apps/gromacs/gromacs-5.0.5/src/gromacs/gmxpreprocess/pdb2gmx.c,
> line: 732
>
> Fatal error:
> Atom OE1 in residue GLU 380 was not found in rtp entry GLU2 with 9
> atoms while sorting atoms.
> -------------------------------------------------------
>
> I made GLU2 and LYS2 based on isopeptide bond, what is the resaon of this
> error?
>

Your coordinate file specifies OE1, the .rtp expects OE.  Fix the name in the 
coordinate file.  Note your GLU2 entry for OE should specify atom type O, not OM.

-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

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