GROMACS version: 2020.02
GROMACS modification: Yes/No
Dear Gromacs users,
I have the pdb file of a neutral alanine aminoacid capped with NH2 and COOH.
I am really struggling to generate the topologies using pdb2gmx, do to atoms no found in rtp files.
The pdb file was generated from an sdf using Avogadro:
This is the file:
COMPND UNNAMED
AUTHOR GENERATED BY OPEN BABEL 2.3.2
ATOM 1 N ALA A 1 -0.966 0.493 1.500 1.00 0.00 N
ATOM 2 CA ALA A 1 0.257 0.418 0.692 1.00 0.00 C
ATOM 3 C ALA A 1 -0.094 0.017 -0.716 1.00 0.00 C
ATOM 4 O ALA A 1 -1.056 -0.682 -0.923 1.00 0.00 O
ATOM 5 CB ALA A 1 1.204 -0.620 1.296 1.00 0.00 C
ATOM 6 OT2 ALA A 1 0.661 0.439 -1.742 1.00 0.00 O
ATOM 7 H1 ALA A 1 -1.383 -0.425 1.482 1.00 0.00 H
ATOM 8 H2 ALA A 1 -0.676 0.661 2.452 1.00 0.00 H
ATOM 9 HA ALA A 1 0.746 1.392 0.682 1.00 0.00 H
ATOM 10 HB1 ALA A 1 1.459 -0.330 2.316 1.00 0.00 H
ATOM 11 HB2 ALA A 1 0.715 -1.594 1.307 1.00 0.00 H
ATOM 12 HB3 ALA A 1 2.113 -0.676 0.697 1.00 0.00 H
ATOM 13 HXT ALA A 1 0.435 0.182 -2.647 1.00 0.00 H
CONECT 1 2 7 8
CONECT 2 1 3 5 9
CONECT 2
CONECT 3 2 4 6
CONECT 4 3
CONECT 5 2 10 11 12
CONECT 5
CONECT 6 3 13
CONECT 7 1
CONECT 8 1
CONECT 9 2
CONECT 10 5
CONECT 11 5
CONECT 12 5
CONECT 13 6
MASTER 0 0 0 0 0 0 0 0 13 0 13 0
END
How could I modify this file accordingly to generate topologies for CHARMM and Amber force fields?
I have tried -ter option but still give me errors.
Thanks in advance,
Lazaro