[gmx-users] H-atoms in .hdb file

[Shima Arasteh]

I tried again as below:
1. defined FOR in .rtp file
2. defined FOR in aminoacids.dat file.
3. chose NH2 as N-Terminal

and then got this topology for FOR and VAL:
; residue   0 FOR rtp FOR  q  0.0
     1        CH1      0    FOR      C      1       0.38     13.019   ; qtot 0.38
     2          O      0    FOR      O      1      -0.38    15.9994   ; qtot 0
; residue   1 VAL rtp VAL  q  0.0
     3         NL      1    VAL      N      2      -0.83    14.0067   ; qtot -0.83
     4          H      1    VAL     H1      2      0.415      1.008   ; qtot -0.415
     5          H      1    VAL     H2      2      0.415      1.008   ; qtot 0
     6        CH1      1    VAL     CA      3          0     13.019   ; qtot 0
     7        CH1      1    VAL     CB      4          0     13.019   ; qtot 0
     8        CH3      1    VAL    CG1      5          0     15.035   ; qtot 0
     9        CH3      1    VAL    CG2      6          0     15.035   ; qtot 0
    10          C      1    VAL      C      7       0.38     12.011   ; qtot 0.38
    11          O      1    VAL      O      7      -0.38    15.9994   ; qtot 0

I guess the topology is correct. Isn't it?


 
Sincerely,
Shima


----- Original Message -----
From: Justin A. Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Cc: 
Sent: Tuesday, June 26, 2012 7:17 PM
Subject: Re: [gmx-users] H-atoms in .hdb file



On 6/26/12 10:44 AM, Shima Arasteh wrote:
>
>
> Thanks for you reply.
> As I explained befor, I need to add a formyl residue to the gmx.ff . I defined it in aminoacid.rtp file and aminoacid.n.tdb .
>
> In .rtp file:
>
>   [ atoms ]
>       C   CH1      0.380  0
>       O     O     -0.380  0
>   [ bonds ]
>       C      O
>       C     +N
>    [angles ]
>    ai    aj    ak
>    O     C     +N
>   [ dihedrals ]
>   O    C   +N   +CA
>
> In .n.hdb file:
>
>   [ replace ]
>       C   CH1      0.380  0
>       O     O     -0.380  0
>   [ bonds ]
>       C      O
>       C     +N

These are the contents of a .n.tdb file, as .n.hdb files do not exist.  You also
do not need such modifications.  If you have the formyl group in the .rtp file,
and it is appropriately defined as "Protein" in residuetypes.dat, then all you
need to do is choose "None" for the N-terminus of the protein.

>
> The first residue after formyl is VAL. I know when VAL is added to FOR, a peptide bond is formed and 1 H-atom is added to the N-atom in this bonding, this H-atom is already defined in .hdb file.
> In my case, an error ( missing H on VAL residue) is occured, thus I decieded to add the H by hand in pdb file.
>

The error probably comes from an incorrect assignment of terminus state.

-Justin

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

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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




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