[gmx-users] Terminal groups problem

[Oleg V. Stroganov]

Hello , Gromacs-users


I have some problem in parameterization of the ligand,
6-aminopenicillanic acid, for GROMOS-96. I have added residue APA
in ffG43a1.rtp and aminoacids.dat. But pdb2gmx does not recognize terminal NH2-
and COO- groups:

pdb2gmx -f apa -o apa -p apa -ter -heavyh  -dummy hydrogens
...
Checking for duplicate atoms....
No N- or C-terminus found: this chain appears to contain no protein
Now there are 1 residues with 14 atoms
...


The APA entry in ffG43a1.rtp begins as follows:

...
[ APA ]
 [ atoms ]
    N     N    -0.28    5; NH2 - ter
    H     H     0.28    5; NH2 - ter
   CA   CH1     0.00    1; 
   CB   CH1     0.00    1;
   SG     S     0.00    1;
   C1     C     0.38    4;
   03     O    -0.38    4;
   N2     N     0.00    1;
  CA2   CH1     0.00    1;
  CB2     C     0.00    1;
  CG1   CH3     0.00    2;
  CG2   CH3     0.00    3;
    C     C     0.38    6; COO - ter
    O     O    -0.38    6; COO - ter
 [ bonds ]
...


Can anyboby explain, how to achieve proper description of the ligand?


-- 
Best regards,
 Oleg Stroganov, Moscow State University.