[gmx-users] Grompp Error (No default Ryckaert-Bell)
David van der Spoel
spoel at xray.bmc.uu.se
Thu Sep 30 11:32:46 CEST 2004
On Wed, 2004-09-29 at 15:24, Pawan Babel wrote:
> Hello Everybody
>
> I am using gromacs (3.2.1) package for my peptide simulation using OPlS
> force field with SPC216 water model.
>
> During grompp i am getting following warnings:
>
> WARNING 1 [file "pep.top", line 1551]:
> No default Ryckaert-Bell. types, using zeroes
> WARNING 2 [file "pep.top", line 2161]:
> No default Ryckaert-Bell. types, using zeroes
>
> Can anyone suggest me how to solve to get rid from warning messages?
> Enclosing important section of my pep.top and pep.pdb files.
> Thanks in Advance
This pep.pdb does not seem to be the right one... You need the file
after running pdb2gmx, since pdb2gmx sorts atoms. It will not change the
error message, but it will tell you which atoms grompp is complaining
about. Then you have to add parameters for these dihedrals (chpater 5 in
the manual).
>
> Regards
> Pawan
>
>
> -----pep.top--------------------------------------------
> line 1543:----> ai aj ak al funct c0 c1
> c2 c3 c4 c5
>
> line 1551: --> 1 5 7 9 3
>
> line 2161: ---> 218 228 230 232 3
>
> --------------------------------------------------------
>
>
> -------------pep.pdb file------------------------------------
> ATOM 1 CH3 ACE 1 1.318 0.000 -0.777 1.00 1.00 1
> ATOM 2 C ACE 1 0.000 0.000 0.000 1.00 1.00 2
> ATOM 3 O ACE 1 0.000 0.000 1.230 1.00 1.00 3
> ATOM 4 1HA ACE 1 1.370 0.890 -1.404 1.00 1.00 4
> ATOM 5 2HA ACE 1 1.370 -0.890 -1.404 1.00 1.00 5
> ATOM 6 3HA ACE 1 2.153 -0.001 -0.075 1.00 1.00 6
> ATOM 7 N GLU 2 -1.092 0.000 -0.750 1.00 1.00 7
> ATOM 8 CA GLU 2 -2.414 0.000 -0.148 1.00 1.00 8
> ATOM 9 C GLU 2 -3.492 0.000 -1.234 1.00 1.00 9
> ATOM 10 O GLU 2 -3.180 0.000 -2.423 1.00 1.00 10
> ATOM 11 CB GLU 2 -2.587 1.192 0.796 1.00 1.00 11
> .....
> ATOM 218 N ASN 14 -44.097 0.000 -6.167 1.00 1.00 218
> ATOM 219 CA ASN 14 -45.399 0.000 -5.521 1.00 1.00 219
> ATOM 220 C ASN 14 -46.494 0.000 -6.590 1.00 1.00 220
> ATOM 221 O ASN 14 -46.200 0.000 -7.784 1.00 1.00 221
> ATOM 222 CB ASN 14 -45.583 1.247 -4.655 1.00 1.00 222
> ATOM 223 CG ASN 14 -45.478 2.520 -5.497 1.00 1.00 223
> ATOM 224 OD1 ASN 14 -46.453 3.028 -6.027 1.00 1.00 224
> ATOM 225 ND2 ASN 14 -44.243 3.006 -5.591 1.00 1.00 225
> ATOM 226 H ASN 14 -44.122 0.000 -7.167 1.00 1.00 226
> ATOM 227 HA ASN 14 -45.496 -0.891 -4.901 1.00 1.00 227
> ATOM 228 1HB ASN 14 -44.822 1.264 -3.875 1.00 1.00 228
> ATOM 229 2HB ASN 14 -46.559 1.212 -4.171 1.00 1.00 229
> ATOM 230 1HD2 ASN 14 -43.487 2.541 -5.131 1.00 1.00 230
> ATOM 231 2HD2 ASN 14 -44.072 3.837 -6.121 1.00 1.00 231
> ATOM 232 N NAC 15 -47.733 0.000 -6.121 1.00 1.00 232
> ATOM 233 CH3 NAC 15 -48.873 0.000 -7.022 1.00 1.00 233
> ATOM 234 H NAC 15 -47.963 0.000 -5.148 1.00 1.00 234
> ATOM 235 HH31 NAC 15 -48.840 -0.890 -7.650 1.00 1.00 235
> ATOM 236 HH32 NAC 15 -48.840 0.890 -7.651 1.00 1.00 236
> ATOM 237 HH33 NAC 15 -49.795 0.001 -6.440 1.00 1.00 237
> TER 238 NAC 15
> END
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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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