[gmx-users] Diagnosing + system blowing up

Shima Arasteh shima_arasteh2001 at yahoo.com
Sun Jul 29 11:55:37 CEST 2012

I listened to you absolutely and didn't proceed any other way!  What I created in .rtp file for  FVAL ( like what you described sometime ago), is  as below:
First of all added the FVAL to residuetyes.dat. 

Then added to .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    H
    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

And at last adding H atoms to .hdb:
1    1    H1    C    N    O
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 tried to follow your suggestion exactly! Believe me! :-)


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> 
Sent: Sunday, July 29, 2012 1:14 AM
Subject: Re: [gmx-users] Diagnosing + system blowing up

On 7/28/12 2:47 PM, Shima Arasteh wrote:
> Dear Mark, Thanks for your suggestions.
> Atom 1 is the C which is expected to connect to the H ( atom 18) . Atom 5 is tha CA of the next resisue ( Valine), the bond 18-5 is not expected at all! However I see this pair in the [pairs] section of topology !
> So I can get the result of an inappropriate bond interaction here! Correct?
> Now I think it's not necessary to go through the diagnosing steps any more! :-(
> What is my duty right now?!
> Is this problem supposed to be fixed in the .pdb file? What's wrong with the pdb file? What about erasing the unexpected bond interactions in topology file?

You'll need to back up and provide more information here.  I recall our discussion several weeks ago about this formylated valine problem, which was solved by creating a special residue called FVAL.  If you created a correct .rtp entry like I described, this shouldn't be happening.

If you're proceeded some other way, you will have to specify exactly what you've done up to this point.  This may require snippets of relevant residues in coordinate files, .rtp entries, etc.  Without this information, everything I've seen thus far is a jumbled mess that is nearly impossible for anyone on this list to troubleshoot.


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

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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