[gmx-users] Re: pdb2gmx error

[Shima Arasteh]

I know it's much better to use a non-deprecated ff.  But what could I do? I have to regenerate the results of simulation done by gmx.ff . Aren't there any solution to pass this step? 

I PROMISE YOU AND ME TO REPEAT THE SIMULATION WHIT A MODERN FF AS SOON AS POSSIBLE :)

 
Sincerely,
Shima


----- Original Message -----
From: Justin A. Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Cc: 
Sent: Wednesday, June 27, 2012 9:55 PM
Subject: Re: [gmx-users] Re: pdb2gmx error



On 6/27/12 12:50 PM, Shima Arasteh wrote:
> OK.
>   PDB FILE IS AS BELOW:
> 
> HETATM    1  C   FOR     0      -0.721   1.600   1.249
> HETATM    2  O   FOR     0      -0.839   2.806   1.453
> ATOM      3  N   VAL     1      -1.227   0.728   2.125
> ATOM      4  CA  VAL     1      -1.918   1.159   3.323
> ATOM      5  C   VAL     1      -1.969   2.678   3.410
> ATOM      6  O   VAL     1      -0.931   3.335   3.447
> ATOM      7  CB  VAL     1      -1.219   0.644   4.576
> ATOM      8  CG1 VAL     1       0.208   1.178   4.618
> ATOM      9  CG2 VAL     1      -1.976   1.118   5.812
> ATOM     10  N   SER     2      -3.181   3.235   3.442
> ATOM     11  CA  SER     2      -3.363   4.671   3.524
> ATOM     12  CB  SER     2      -4.138   5.196   2.320
> ATOM     13  OG  SER     2      -4.296   6.612   2.437
> ATOM     14  C   SER     2      -4.135   5.054   4.778
> ATOM     15  O   SER     2      -5.272   4.628   4.966
> 
> 

The error comes from the VAL residue (residue 2 in the sequence based on the internal numbering used by pdb2gmx, as I suspected earlier).  Note the following line in the [impropers] section of aminoacids.rtp in the [VAL] entry:

   -C   -CA     N    -O

The improper is defined using the position of a CA atom in the preceding residue, which in this case does not exist because it is not a normal amino acid (though an ACE cap will also work because its atoms are named suitably).  This method of defining the improper is somewhat odd.  Using a more modern force field like Gromos96 53a6 does not give rise to this error, as all impropers are defined using only -C or +N.  Just another reason to use a non-deprecated force field :)

-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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