[gmx-users] termini modification

Vijayaraj vijayaraj81 at gmail.com
Sat Aug 27 12:17:29 CEST 2011


I am using gromacs 4.5.4 with amber99sb ff. I would like to modify the
terminal residues from NALA and CALA to normal ALA (just as middle
residues). As the terminal selection option is not enabled with the amber
ff, I am using the termini modification parameters with aminoacids.c.tdb.
here is my code for the aminoacids.c.tdb

[ COO- ]

[ replace ]
H    H    1.00800        0.27190
N    N    14.01000    -0.41570
CA    CT    12.01000    0.03370
HA    H1    1.00800        0.08230
C    C    12.01000    0.59730
CB    CT    12.01        -0.1825
HB1    HC    1.008        0.0603
HB2    HC    1.008        0.0603
HB3    HC    1.008        0.0603

[ add ]
1    1    O    C    CA    N
        O    16.00000    -0.56790

[ bonds ]
C    O     1    0.12290        476976.0

[ delete ]

when I run pdb2gmx using this termini modification, everything works fine
except the deletion of OC1 and OC2 atoms, the error which I get for this run
as follows,

Fatal error:
Atom OC2 not found in residue seq.nr. 8 while adding atom

any suggestion to delete the OC1 and OC2 atoms. If I dont enable this [
delete ] option with the aminoacids.c.tdb file, it works fine by adding the
O atom to the terminal residue including the presence of OC1 and OC2 atoms.
first I am trying to modify the c terminal residue.

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