[gmx-users] Error by pdb2gmx

[Yanmei Song]

Dear All users:

I was trying to set up a long chain polymer system. I got the
following PDB file from WebLab. How can I make changes to the file in
order to make it as a GROMACS input pdb file. Then I can use pdb2gmx
to get the gro, itp and top file.

When I perform the pdb2gmx command, I got the error message:

Residue 'MOL' not found in residue topology database

Thank you in advance!

REMARK   Created:  Tue Apr 28 15:02:20 US Mountain Standard Time 2009
ATOM      1 Si1  MOL A   1       3.798   2.502  -0.836  1.00  0.00
ATOM      2  O2  MOL A   1       4.664   1.185  -0.027  1.00  0.00
ATOM      3 Si4  MOL A   1       4.900  -0.177   1.079  1.00  0.00
ATOM      4  O6  MOL A   1       3.689  -1.438   0.845  1.00  0.00
ATOM      5 Si7  MOL A   1       2.039  -2.056   0.903  1.00  0.00
ATOM      6  O8  MOL A   1       2.039  -3.722   0.332  1.00  0.00
ATOM      7 Si9  MOL A   1       1.180  -5.224   0.014  1.00  0.00
ATOM      8  O10 MOL A   1       2.298  -6.420  -0.633  1.00  0.00
ATOM      9 Si16 MOL A   1       3.361  -7.028  -1.900  1.00  0.00
ATOM     10  O17 MOL A   1       4.535  -5.799  -2.365  1.00  0.00
ATOM     11 Si18 MOL A   1       5.953  -5.366  -3.320  1.00  0.00
ATOM     12  O22 MOL A   1       6.258  -3.639  -3.185  1.00  0.00
ATOM     13 Si24 MOL A   1       5.682  -1.999  -3.453  1.00  0.00
ATOM     14  O26 MOL A   1       6.881  -0.844  -2.890  1.00  0.00
ATOM     15 Si28 MOL A   1       8.517  -0.212  -3.003  1.00  0.00
ATOM     16  O29 MOL A   1       8.809   0.341  -4.647  1.00  0.00
ATOM     17 Si30 MOL A   1       9.880   1.056  -5.847  1.00  0.00
ATOM     18  C34 MOL A   1       9.732  -1.565  -2.571  1.00  0.00
ATOM     19  C36 MOL A   1       8.724   1.219  -1.818  1.00  0.00
ATOM     20  C38 MOL A   1       6.589  -0.910   0.760  1.00  0.00
ATOM     21  C40 MOL A   1       4.840   0.411   2.849  1.00  0.00
ATOM     22  C42 MOL A   1       5.390  -1.733  -5.281  1.00  0.00
ATOM     23  C44 MOL A   1       4.081  -1.754  -2.530  1.00  0.00
ATOM     24  C46 MOL A   1       7.438  -6.318  -2.702  1.00  0.00
ATOM     25  C48 MOL A   1       5.648  -5.792  -5.115  1.00  0.00
ATOM     26  C50 MOL A   1       2.341  -7.493  -3.396  1.00  0.00
ATOM     27  C52 MOL A   1       4.255  -8.543  -1.268  1.00  0.00
ATOM     28  C54 MOL A   1       0.463  -5.865   1.617  1.00  0.00
ATOM     29  C56 MOL A   1      -0.202  -4.925  -1.209  1.00  0.00
ATOM     30  C58 MOL A   1       1.433  -2.009   2.671  1.00  0.00
ATOM     31  C60 MOL A   1       0.903  -1.026  -0.161  1.00  0.00
ATOM     32  O62 MOL A   1       3.060   3.615   0.318  1.00  0.00
ATOM     33 Si63 MOL A   1       1.891   3.996   1.583  1.00  0.00
ATOM     34  O64 MOL A   1       2.107   5.670   2.078  1.00  0.00
ATOM     35 Si68 MOL A   1       3.135   6.928   2.750  1.00  0.00
ATOM     36  C69 MOL A   1       3.667   6.449   4.477  1.00  0.00
ATOM     37  C72 MOL A   1       5.024   3.447  -1.883  1.00  0.00
ATOM     38  C74 MOL A   1       2.469   1.818  -1.953  1.00  0.00
ATOM     39  C76 MOL A   1       0.160   3.770   0.914  1.00  0.00
ATOM     40  C78 MOL A   1       2.129   2.878   3.056  1.00  0.00
ATOM     41  C80 MOL A   1       2.186   8.538   2.814  1.00  0.00
ATOM     42 Si84 MOL A   1       4.912   7.172   1.476  1.00  0.00
ATOM     43  C84 MOL A   1       8.985   1.172  -7.484  1.00  0.00
ATOM     44  C86 MOL A   1      10.388   2.767  -5.292  1.00  0.00
ATOM     45  C88 MOL A   1      11.402  -0.013  -6.044  1.00  0.00
TER


-- 
Yanmei Song
Department of Chemical Engineering
ASU