[gmx-users] How to cap a peptide using pdb2gmx

[Camilo Andrés Jimenez Cruz]

Hi everybody

I downloaded a pdb entry from RCSB and it comes with charged terminii,
for example, the first aminoacid is


ATOM      1  N   ASN A   1      -8.901   4.127  -0.555  1.00  0.00           N
ATOM      2  CA  ASN A   1      -8.608   3.135  -1.618  1.00  0.00           C
ATOM      3  C   ASN A   1      -7.117   2.964  -1.897  1.00  0.00           C
ATOM      4  O   ASN A   1      -6.634   1.849  -1.758  1.00  0.00           O
ATOM      5  CB  ASN A   1      -9.437   3.396  -2.889  1.00  0.00           C
ATOM      6  CG  ASN A   1     -10.915   3.130  -2.611  1.00  0.00           C
ATOM      7  OD1 ASN A   1     -11.269   2.700  -1.524  1.00  0.00           O
ATOM      8  ND2 ASN A   1     -11.806   3.406  -3.543  1.00  0.00           N
ATOM      9  H1  ASN A   1      -8.330   3.957   0.261  1.00  0.00           H
ATOM     10  H2  ASN A   1      -8.740   5.068  -0.889  1.00  0.00           H
ATOM     11  H3  ASN A   1      -9.877   4.041  -0.293  1.00  0.00           H
ATOM     12  HA  ASN A   1      -8.930   2.162  -1.239  1.00  0.00           H
ATOM     13  HB2 ASN A   1      -9.310   4.417  -3.193  1.00  0.00           H
ATOM     14  HB3 ASN A   1      -9.108   2.719  -3.679  1.00  0.00           H
ATOM     15 HD21 ASN A   1     -11.572   3.791  -4.444  1.00  0.00           H
ATOM     16 HD22 ASN A   1     -12.757   3.183  -3.294  1.00  0.00           H

and the same goes for the last one

I need to use ACE and NME for the terminii, so I tried using the -ter
option in the pdb2gmx command, but when I use it it says
N-terminus: none
C-terminus: none
and don't let me choose any terminii.

Any ideas.

Thanks in advance

--
Camilo Andrés Jiménez Cruz