[gmx-users] Incorrect bond in top file

[Shima Arasteh]

OK, I checked the bonds section of top, there  is no bond between CN and HN.  

Thanks for it.

But there is a new problem. 

I passed the steps for simulation the protein in water, up to the EM step. I ran grompp and then mdrun to do energy minimization. I see the protein broken. As you said in another email asked a few hours ago, I ran the command trjconv :
# trjconv -s EM.tpr -f EM.gro -pbc mol -ur compact -o EM_pbc.gro

I still see the protein broken.The FVAL is not connected to the next residue. Would you let me know your idea? Is there any trick here?


 
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 11:08 PM
Subject: Re: [gmx-users] Incorrect bond in top file



On 8/27/12 2:35 PM, Shima Arasteh wrote:
> Please take a look at the .top file generated:
> 
> 
>       1          C      1   FVAL     CN      1      0.357     12.011   ; qtot 0.357
>       2         HA      1   FVAL     H1      2        0.1      1.008   ; qtot 0.457
>       3          O      1   FVAL     ON      3      -0.51     15.999   ; qtot -0.053
>       4        NH1      1   FVAL      N      4     -0.423     14.007   ; qtot -0.476
>       5          H      1   FVAL     HN      5      0.333      1.008   ; qtot -0.143
>       6        CT1      1   FVAL     CA      6      0.034     12.011   ; qtot -0.109
>       7         HB      1   FVAL     HA      7       0.09      1.008   ; qtot -0.019
>       8        CT1      1   FVAL     CB      8     -0.093     12.011   ; qtot -0.112
>       9         HA      1   FVAL     HB      9       0.09      1.008   ; qtot -0.022
>      10        CT3      1   FVAL    CG1     10     -0.268     12.011   ; qtot -0.29
>      11         HA      1   FVAL   HG11     11       0.09      1.008   ; qtot -0.2
>      12         HA      1   FVAL   HG12     12       0.09      1.008   ; qtot -0.11
>      13         HA      1   FVAL   HG13     13       0.09      1.008   ; qtot -0.02
>      14        CT3      1   FVAL    CG2     14     -0.268     12.011   ; qtot -0.288
>      15         HA      1   FVAL   HG21     15       0.09      1.008   ; qtot -0.198
>      16         HA      1   FVAL   HG22     16       0.09      1.008   ; qtot -0.108
>      17         HA      1   FVAL   HG23     17       0.09      1.008   ; qtot -0.018
>      18          C      1   FVAL      C     18      0.528     12.011   ; qtot 0.51
>      19          O      1   FVAL      O     19      -0.51     15.999   ; qtot 0
> ; residue   2 SER rtp SER  q  0.0
>      20        NH1      2    SER      N     20      -0.47     14.007   ; qtot -0.47
> 
> I visualized the .gro file, found CN-HN bond.
> 

What appears in a visualization program is irrelevant.  They all have algorithms designed to guess what's connected by distance search, or some variation thereof.  What's definitive is the [bonds] section of the topology.  If that says there is a bond between the two atoms in question, then there's a problem.  From the .rtp and .hdb entries, I can see no reason why pdb2gmx would make a bond.

-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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