[gmx-users] FF 43a1 - Residue Name / Editor Prob?

[Justin A. Lemkul]

Marc Charendoff wrote:
> Hey all,
> 
>      I am trying to pdb2gmx a pdb file using the 43a1 force field and 
> despite my checking the .atp and .rtp files, I still get the following 
> error . . .
> 
> Back Off! I just backed up posre_A.itp to ./#posre_A.itp.2#
> Processing chain 2 '+' (2 atoms, 1 residues)

This is a good clue - pdb2gmx is finding a chain called "+" even though your 
structure is chain "A" - your format is incorrect.

<snip>

> 
> *BUT . . . . I thought I DID use ZN2+.   * 
> 
> ATOM   1912  CG2 ILE A 240      22.637  28.530  -5.925  1.00 16.18     
>  .000  
> ATOM   1913  CD1 ILE A 240      22.075  30.322  -3.413  1.00 16.47     
>  .000  
> ATOM   1914  ZN2+ ZN2+ A 241    11.832  23.652  11.052  1.00 20.05     
>  .000  

If you have a four-character atom name, you have to offset the start of the atom 
name by -1, so the alignment should be:

  CD1
ZN2+

not:

  CD1
  ZN2+

-Justin

> ATOM   1915  ZN2+ ZN2+ A 242    11.551  25.149  14.101  1.00 23.28     
>  .000  
> ATOM   1916  O   HOH A 243      11.793  23.332  13.260  1.00 19.06     
>  .000  
> ATOM   1917  HW1 HOH A 243      12.609  23.332  13.837  1.00  0.00
> ATOM   1918  HW2 HOH A 243      10.977  23.332  13.837  1.00  0.00
> END
> 
> Any guidance you could  provide would be appreciated.
> 
> Thanks, Marc
> 
> 
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> 
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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