[gmx-users] question

[Justin Lemkul]

On 5/19/15 2:45 PM, Andrew Bostick wrote:
> Dear Justin
>
> Based on your answer (You don't want to be adding 2 HZ here, just one
> since it is a peptide bond.), I modified LYS2 in aminoacids.hdb file
>
> LYS2     2
> 1 1 H N -C CA
> 1 4 HZ NZ CE CD
>
> But, after pdb2gmx, I encountered with
>
> WARNING: atom HZ1 is missing in residue LYS 540 in the pdb file
>           You might need to add atom HZ1 to the hydrogen database of
> building block LYS2
>           in the file aminoacids.hdb (see the manual)
>
>
> WARNING: atom HZ2 is missing in residue LYS 540 in the pdb file
>           You might need to add atom HZ2 to the hydrogen database of
> building block LYS2
>           in the file aminoacids.hdb (see the manual).
>
> What is the reason of this issue? Is there problem in my rtp file (about
> LYS2 and GLU2 entries)?
>

Yes.  This:

> [ 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     2
>     NZ    NT    -0.28000     3
>    HZ1     H     0.28000     3
>    HZ2     H     0.00000     3

Here, you specify two HZ atoms, when you actually only want one (look at the 
structure of a peptide bond!).  The .hdb entry specifies one HZ to be built 
(with the name HZ), but your .rtp tells pdb2gmx there should be two, HZ1 and 
HZ2.  That, of course, is not correct, as is assigning a zero charge to any H 
atom here.

-Justin

>      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   HZ1    gb_2
>     NZ   HZ2    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   HZ1     ga_10
>     CE    NZ   HZ2     ga_10
>    HZ1    NZ   HZ2     ga_9
>   [ 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   HZ1     gd_14
>
> Thanks in advance.
>

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

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

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