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

Shima Arasteh shima_arasteh2001 at yahoo.com
Tue Jun 26 16:44:35 CEST 2012

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 

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.

Any suggestion please?

Thanks so much.


----- Original Message -----
From: Justin A. Lemkul <jalemkul at vt.edu>
To: Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Tuesday, June 26, 2012 6:58 PM
Subject: Re: [gmx-users] H-atoms in .hdb file

On 6/26/12 10:25 AM, Shima Arasteh wrote:
>   Dear gmx users,
> However this H-atom is defined in .hdb file of force field before, why sometimes I need to add a H-atom to the pdb on my own?

A properly constructed .hdb entry eliminates the need for manual introduction of 
H atoms.  If you aren't achieving the desired behavior, you will have to be a 
lot more specific about what you're doing and what you're observing.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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