[gmx-users] pdb2gmx error

[Justin A. Lemkul]

Ilya Chorny wrote:
> I created a new ffoplsaa.rtp entry for ASN with a polysacharide attached 
> to the side chain nitrogen called ASBG. I want to test the new residue 
> by itself.
> 
> When I pdb2gmx it I get the following error.
> 
> -------------------------------------------------------
> Program pdb2gmx, VERSION 4.0.3
> Source code file: pgutil.c, line: 87
> 
> Fatal error:
> Atom N not found in residue 1094904186 while adding improper
> 
> -------------------------------------------------------
> 

If the residue is by itself, something is seriously wrong if pdb2gmx is 
detecting a billion residues!

> If I comment out 
> 
>  CA    +N     C     O     improper_O_C_X_Y
> 

Right, because if the residue is by itself, there will be no N in the next 
residue (+N).

> Then pdb2gmx creates the gro and top with no error messages.
> 
> I saw an much earlier post by Justin with a similar error message but no 
> resolution. Anyone have anythoughts?
> 

IIRC, that was in reference to version 3.3.1, which turned out to be the result 
of a broken Ubuntu package, and was not a problem with Gromacs itself.

Try it in the context of the actual molecule, if topology construction requires 
the next residue.  In isolation, that residue will always fail with +N.

-Justin

> Thanks,
> 
> Ilya
> 
> 
> 
> 
> -- 
> Ilya Chorny Ph.D.
> 
> 
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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
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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