[gmx-users] grompp and [ ?types ]

[David L. Bostick]

For this residue I find nothing wrong with the angles, but only with the
dihedral you mentioned 

     1     5     7    17     2
>     N    CA     CB   C (names)
>    NL    C1     C2   C (types)

The list of impropers for GLUH in the .rtp file is 

     N    -C    CA     H
    CA     N     C    CB
    CD   OE1   OE2    CG
    -C   -CA     N    -O 

And does not include the erroneous dihedral.  I don't know why pdb2gmx
thinks it should be there.

The angles and other proper dihedrals that I get errors for are only a
result of having those silly HC atoms on the C3's .  I will probably just
go back to the plain ffgmx, since I'm really not interested in NMR analysis
stuff.

David
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
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, David van der Spoel wrote:

> On Fri, 19 Apr 2002, Erik Lindahl wrote:
> 
> >>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
> I pasted this into a file and ran
> pdb2gmx -inter
> and selected the ffgmx2 force field and a protonated GLU. One problem with
> grompp (one improper not found):
>     1     5     7    17     2
>     N    CA     CB   C (names)  
>    NL    C1     C2   C (types)
> 
> nothing with angles. What am I doing differently?
> 
> Groeten, David.
> ________________________________________________________________________
> Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
> Husargatan 3, Box 576,  	75123 Uppsala, Sweden
> phone:	46 18 471 4205		fax: 46 18 511 755
> spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> 
> 
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