[gmx-users] pdb2gmx error

[Justin A. Lemkul]

Ilya Chorny wrote:
> 
> 
> On Sat, Mar 14, 2009 at 10:03 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     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!
> 
> 
> I'll checkmy file again. 
> 
> 
> 
>         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).
> 
> 
> If this is true then pdb2gmx will crash evertime it is run on an 
> isolated AA, which it doesn't. 
> 

Not if pdb2gmx recognizes how to treat termini.  If you are using non-standard 
residues and creating new linkages between polymers, then you may encounter 
problems.  Perhaps the problem relates the actual residue itself, have you added 
ASBG to aminoacids.dat?  You haven't showed us your pdb2gmx command line, so we 
can only assume that something is not being done correctly.

-Justin

> 
> 
>         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 <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
>     ========================================
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> 
> 
> 
> -- 
> Ilya Chorny Ph.D.
> 

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

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

========================================