[gmx-users] Incorrect bond in top file

[Justin Lemkul]

On 8/27/12 1:31 PM, Shima Arasteh wrote:
> :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
>

I see nothing out of the ordinary here.  You're saying that HN is bonded to CN 
after running pdb2gmx?

-Justin

>
>
> 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
>

-- 
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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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