[gmx-users] grompp and [ ?types ]

[David van der Spoel]

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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