[gmx-users] grompp and [ ?types ]

[David L. Bostick]

I know about ffgmx2's hydrogens, but they look so pretty on top of those
aliphatic carbons! .. :)

I also have normal GLU residues on my protein.  The same entries for
improper dihedrals occur in the ffgmx.rtp for GLU as for GLUH.  However,
this improper is not among those in the entries for either, so I just
manually deleted it.

Thanks,
David

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David Bostick					Office: 262 Venable Hall
Dept. of Physics and Astronomy			Phone:  (919)962-0165 
Program in Molecular and Cellular Biophysics 
UNC-Chapel Hill					
CB #3255 Phillips Hall				dbostick at physics.unc.edu	
Chapel Hill, NC 27599	           		http://www.unc.edu/~dbostick	
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On Fri, 19 Apr 2002, Erik Lindahl wrote:

> David L. Bostick wrote:
> 
> >Hi Erik,
> >
> >The original entry  for the GLU from the original PDB file that becomes
> >GLUH after pdb2gmx is:
> >ATOM   1544  N   GLU   235      87.687  40.544  16.986  1.00 80.74
> >ATOM   1545  CA  GLU   235      87.395  40.535  15.564  1.00 84.24
> >ATOM   1546  C   GLU   235      86.875  39.183  15.064  1.00 86.12
> >ATOM   1547  O   GLU   235      85.770  39.098  14.523  1.00 87.14
> >ATOM   1548  CB  GLU   235      88.645  40.908  14.772  1.00 87.92
> >ATOM   1549  CG  GLU   235      89.234  42.276  15.070  1.00 99.37
> >ATOM   1550  CD  GLU   235      90.506  42.517  14.263  1.00112.58
> >ATOM   1551  OE1 GLU   235      90.418  42.566  13.015  1.00113.76
> >ATOM   1552  OE2 GLU   235      91.596  42.636  14.871  1.00115.15
> >
> Hi,
> 
> I get exactly the same error, and you're right that there doesn't seem 
> to be any good reason...  Berk is the mastermind of pdb2gmx, so we'll 
> see if he has any ideas!
> 
> In any case, I'm working on incorporating the OPLS-AA forcefield now, so 
> hopefully you can use that soon (and I'll probably stumble upon the bug 
> on the way :-). The ffgmx2 force field isn't a normal all-atom 
> forcefield; the hydrogens are just intended for NMR restraints.
> 
> Cheers,
> 
> Erik
> 
> 
> 
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