[gmx-users] pdb2gmx error

[Ilya Chorny]

On Sat, Mar 14, 2009 at 10:03 PM, Justin A. Lemkul <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.

>
>
>  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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>>
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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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-- 
Ilya Chorny Ph.D.
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