[gmx-users] Capping the termini of a protein

[soumadwip ghosh]

Hi,
    I wish to simulate a protein in the presence of 8M Urea using the
OPLS-AA force field. I did the capping of the end termini of the protein
HP36 in the following way:

1. I acylated the last residue no.76 (PHE) and methylated the N-terminus of
the residue 41 (MET) using the molfracture utility of VMD.

2. In the corresponding pdb file I named the two terminal residues as NAC
and ACE. Here is the snippet of the parts of the pdb file I am using.

ATOM      1  C   NAC A  41       1.161 -10.533  -4.908  0.80  2.37
  C
ATOM      2  H   NAC A  41       1.023 -11.636  -4.912  0.80  2.53
  H
ATOM      3  H   NAC A  41       0.323 -10.081  -5.481  0.80  0.00
  H
ATOM      4  H   NAC A  41       2.114 -10.304  -5.433  0.80  0.00
  H
ATOM      5  N   MET A  41       1.177 -10.035  -3.493  1.00  2.04
  N
ATOM      6  CA  MET A  41       0.292  -8.839  -3.377  1.00  1.55
  C
ATOM      7  C   MET A  41      -0.488  -8.912  -2.063  1.00  1.22
  C
ATOM      8  O   MET A  41      -1.039  -9.937  -1.709  1.00  1.32
  O
ATOM      9  CB  MET A  41      -0.674  -8.793  -4.565  1.00  1.98
  C
ATOM     10  CG  MET A  41      -0.091  -7.889  -5.657  1.00  2.27
  C
ATOM     11  SD  MET A  41      -0.153  -8.747  -7.255  1.00  3.04
  S
ATOM     12  CE  MET A  41      -0.971  -7.432  -8.193  1.00  3.78
  C
ATOM     13  H1  MET A  41       0.835 -10.784  -2.856  1.00  2.30
  H
ATOM     14  C   NAC A  41       1.161 -10.533  -4.908  0.80  2.37
  C
..............


ATOM    580  N   PHE A  76       5.995  -7.109   3.616  1.00  2.54
  N
ATOM    581  CA  PHE A  76       6.033  -8.575   3.923  1.00  3.42
  C
ATOM    582  C   PHE A  76       4.678  -9.203   3.574  1.00  4.09
  C
ATOM    583  O   PHE A  76       3.672  -8.540   3.760  1.00  4.51
  O
ATOM    584  CB  PHE A  76       6.311  -8.794   5.413  1.00  4.10
  C
ATOM    585  CG  PHE A  76       7.511  -9.689   5.590  1.00  4.58
  C
ATOM    586  CD1 PHE A  76       7.383 -11.078   5.459  1.00  4.90
  C
ATOM    587  CD2 PHE A  76       8.749  -9.126   5.900  1.00  5.16
  C
ATOM    588  CE1 PHE A  76       8.501 -11.901   5.639  1.00  5.67
  C
ATOM    589  CE2 PHE A  76       9.865  -9.944   6.085  1.00  5.89
  C
ATOM    590  CZ  PHE A  76       9.742 -11.331   5.955  1.00  6.09
  C
ATOM    591  OXT PHE A  76       4.671 -10.340   3.131  1.00  4.57
  O
ATOM    592  H   PHE A  76       5.549  -6.495   4.231  1.00  2.57
  H
ATOM    593  HA  PHE A  76       6.809  -9.044   3.338  1.00  3.50
  H
ATOM    594  HB2 PHE A  76       6.513  -7.843   5.882  1.00  4.22
  H
ATOM    595  HB3 PHE A  76       5.448  -9.255   5.880  1.00  4.61
  H
ATOM    596  HD1 PHE A  76       6.424 -11.517   5.220  1.00  4.87
  H
ATOM    597  HD2 PHE A  76       8.834  -8.058   5.998  1.00  5.33
  H
ATOM    598  HE1 PHE A  76       8.404 -12.974   5.540  1.00  6.17
  H
ATOM    599  HE2 PHE A  76      10.822  -9.507   6.326  1.00  6.53
  H
ATOM    600  HZ  PHE A  76      10.604 -11.962   6.103  1.00  6.80
  H
ATOM    601  C   ACE A  76       6.083 -10.840   3.046  0.80  0.00
  C
ATOM    602  H   ACE A  76       6.454 -11.080   4.065  0.80  0.00
  H
ATOM    603  H   ACE A  76       6.142 -11.764   2.432  0.80  0.00
  H
ATOM    604  H   ACE A  76       6.760 -10.077   2.604  0.80  0.00
  H
END


I edited the pdb obtained from molfracture a little bit because the entries
corresponding to all NAC and ACE atoms were shuffled. Is the above syntax
right?

When I issue :
pdb2gmx -f my.pdb -o init.gro -ignh -ter, I was asked for selecting two
termini charges. It was none for both the cases.

But the topology was not created due to the following error:

Fatal error:
There is a dangling bond at at least one of the terminal ends. Fix your
coordinate file, add a new terminal database entry (.tdb), or select the
proper existing terminal entry.


Is there any suggestion to solve this? Can anybody tell me what should be
the correct format of the configuration file?

Thanks for your help in advance.

Soumadwip Ghosh
IITB, Mumbai
India