[gmx-users] Problem with encad in pdb2gmx, GMX 3.3 CVS version. Posible Bug in ffencads-c.tdb file?

[David van der Spoel]

Leonardo Sepulveda Durán wrote:
> Hello!!!
> 
> A few weeks ago I posted an error I got using pdb2gmx and encads :
> 
> pdb2gmx  -f S1.pdb -ignh
> 
> OUTPUT:
> 
> Number of bonds was 1059, now 1059
> Generating angles, dihedrals and pairs...
> Before cleaning: 2808 pairs
> -------------------------------------------------------
> Program pdb2gmx, VERSION 3.3
> Source code file: pgutil.c, line: 87
> 
> Fatal error:
> Atom CB not found in residue 64 while adding improper
> 
> -------------------------------------------------------
> 
> The file numbering begins with 20, and end in 83, so the trouble is in
> the last residue. I checked the presence of two oxigen atoms, but
> leaving only one do not solve the trouble.
> 
> whwn I use other protein the program works. Then I cut that protein on
> a GLY residue, giving this terminal atoms
> 
> ATOM    315  N   GLY    39       5.478  39.842  35.478  1.00 13.50      1ENH 376
> ATOM    316  CA  GLY    39       6.343  40.900  35.994  1.00 12.21      1ENH 377
> ATOM    317  C   GLY    39       5.897  41.429  37.359  1.00 12.24      1ENH 378
> ATOM    318  O   GLY    39       6.219  42.547  37.738  1.00 11.54      1ENH 379
> TER     419         GLY    39                                         
>     1ENH 528
> END
> 
> The error appear again. I think this would be a bug regarding the
> patching of terminal glycines using encad (this dont happen using
> OPLS). I tried to track the error, but pgutil.c only have subroutines
> for printing.   Looking at ffencads-c.tdb this appears
> 
> [ COO- ]
> [ replace ]
> C               Abis    12.011  0.84
> [ add ]
> 2       8       O       C       CA      N
>         Obis    15.9994 -0.92
> [ delete ]
> O
> [ dihedrals ]
> N       CA      C       O2
> [ impropers ]
> CA      O2      C       O1      improper_X_X_A_X
>  N       C       CA      CB      improper_X_X_C_X
> 
> It seems the last line is the problem, the program try to delete that
> improper but it cant find a CB atom in Glycines. The OPLS file for
> patches (ffoplsaa-c.tdb), is longer, it have special treatments for
> GLY and PRO.
> 
> I delete the last line (N       C       CA      CB     
> improper_X_X_C_X) and the problem was solved. Nevertheless, this would
> be detrimental for other residues with CB atoms, and I really dont
> know if my fix would give another trouble. Can someone help? Erik?
> David?

It seems like an extra entry in the tdb file is necessary for Gly and to 
use the -ter flag. Alternative would be to change the code such that 
non-existant dihedrals would not be removed. The first solution is 
simpler (for us) of course.

> 
> Leonardo
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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