[gmx-users] pdb2gmx error

Tsjerk Wassenaar tsjerkw at gmail.com
Sun Mar 15 22:57:57 CET 2009


>>        -------------------------------------------------------
>>        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.



Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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