[gmx-users] pdb2gmx error

Ilya Chorny ichorny at gmail.com
Sun Mar 15 23:59:44 CET 2009

Thanks, this very helpful!!!

Sent from my iPhone

On Mar 15, 2009, at 3:48 PM, "Justin A. Lemkul" <jalemkul at vt.edu> wrote:

> Tsjerk Wassenaar wrote:
>> Hi,
>>>>       -------------------------------------------------------
>>>>       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
>>>>       -------------------------------------------------------
>> This could well be something platform/compiler related. I think it
>> comes pretty close to the maximum for a signed int.
>>>>       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.
>> This is not correct. Okay, you got me doubt myself a bit, so I tested
>> and had HOH include a bond from OW to +OW. It's not in either .tdb,  
>> so
>> according to Justin it would fail by itself. But it doesn't. pdb2gmx
>> neglects references to other residues if these residues are not
>> present. So something else is wrong. However, for us to be able to
>> help, a more complete account of the problem is necessary. The best
>> thing to do is to send the .rtp entry and the coordinates, if you're
>> not too sensitive about them being archived while your just working  
>> on
>> them. Also, do provide details regarding version, platform, shoe size
>> and anything else that may seem appropriate to diagnose the problem.
>> Cheers,
>> Tsjerk
> Thanks to Tsjerk for pointing out a mistake on my part.  Apologies  
> for being inarticulate.  What I was really getting at was that I  
> have seen random errors (and not necessarily this one in particular)  
> resulting from not including amino acids in aminoacids.dat.  For  
> example, I have used some non-standard amino acids in some  
> simulations and seen similar errors when pdb2gmx did not know they  
> should be linked like amino acids.  So there are two things I'd  
> suggest considering, in addition to the information that Tsjerk  
> suggested:
> 1. Add ASBG to aminoacids.dat
> 2. Consider whether or not you need to make an entry into  
> specbond.dat; if the polymer is connected through the side chain as  
> you initially said, then you may have to define a special bond or  
> atom name to discern this amide bond from the one present in the  
> backbone of the amino acid.
> -Justin
> -- 
> ========================================
> 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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