[gmx-users] Incorrect bond in top file

[Shima Arasteh]

:D
Hope so ( for your caps lock )! ;)
Thanks, I'm happy!

The relevant rtp file:


[ FVAL ]
 [ atoms ]
    CN    C     0.357    0
    ON    O    -0.51    1
    H1    HA    0.100    2
    N    NH1    -0.423    3
    HN    H    0.333    4
    CA    CT1    0.034    5
    HA    HB    0.09    6
    CB    CT1    -0.093    7
    HB    HA    0.09    8
    CG1    CT3    -0.268    9
    HG11    HA    0.09    10
    HG12    HA    0.09    11
    HG13    HA    0.09    12
    CG2    CT3    -0.268    13
    HG21    HA    0.09    14
    HG22    HA    0.09    15
    HG23    HA    0.09    16
    C    C    0.528    17
    O    O    -0.510    18
 [ bonds ]
    CN    H1
    CN    ON
    CN    N
    N    HN
    CA    N
    CA    HA
    CA    C
    C    O
    CA    CB
    CB    HB
    CB    CG1
    CB    CG2
    CG2    HG21
    CG2    HG22
    CG2    HG23
    CG1    HG11
    CG1    HG12
    CG1    HG13
     
 [ impropers ]
    CN     N    ON    H1

The relevant .hdb file:

 FVAL    6
1    1    H1    CN    N    ON
1    1    HN    N    C    CA
1    5    HA    CA    N    C    CB
1    5    HB    CB    CA    CG1    CG2
3    4    HG1    CG1    CB    CA
3    4    HG2    CG2    CB    CA



Sincerely,
Shima


----- Original Message -----
From: Justin Lemkul <jalemkul at vt.edu>
To: Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org>
Cc: 
Sent: Monday, August 27, 2012 8:39 PM
Subject: Re: [gmx-users] Incorrect bond in top file



On 8/27/12 11:41 AM, Shima Arasteh wrote:
>
>
> Dear users,
>
>
> [ Especially dear Justin ( please don't shout at me! ) ],
>

I haven't, and won't.  I keep my caps lock off ;)  Hopefully no one gets the 
impression that I have done otherwise...

>
> As I have described it many times, I defined a new residue named FVAL in aminoacids.rtp of the force field ( CHARMM36). The first step is "generating top file". When I ran the command of pdb2gmx, the top file is generated, but it contains a bond which I have not defined in the FVAL. The incorrect bond is between H-atom of valine (  this H is one of the atoms connected to the N of valine and this N is in the backbone, The N of valine is connected to C of formyl, CA and H)  and C-atom of formyl group! ( It seems that the C of formyl doesn't form a second ordered bond with O ).
>
> aminoacids.hdb and aminoacids.rtp are the files I modified.
>

Please post the relevant .rtp and .hdb entries.  There is an error somewhere, 
but we can't determine what it is without seeing these.

-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

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