C-terminal COO-

User discussions
1

GROMACS version: 2020.1
GROMACS modification: Yes/No

Hi,
I am building my system using pdb2gmx with charmm36m ff.

gmx pdb2gmx -f <input.pdb> -o <output.gro> -ter

While choosing the C-terminus type to COO- it shows the following error.
Fatal error:
Residue 391 named GLY of a molecule in the input file was mapped
to an entry in the topology database, but the atom CB used in
that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fixed.
But my C-ter GLY looks fine.

:
:
ATOM   6232  N   SER B 406     -51.587  90.298  61.259  1.00 30.00           N
ATOM   6233  CA  SER B 406     -52.299  91.039  62.324  1.00 30.00           C
ATOM   6234  C   SER B 406     -51.317  91.980  63.024  1.00 30.00           C
ATOM   6235  O   SER B 406     -50.465  91.490  63.789  1.00 30.00           O
ATOM   6236  CB  SER B 406     -52.925  90.080  63.293  1.00 30.00           C
ATOM   6237  OG  SER B 406     -53.770  89.162  62.614  1.00 30.00           O
ATOM   6238  N   GLY B 407     -51.432  93.280  62.747  1.00 30.00           N
ATOM   6239  CA  GLY B 407     -50.591  94.300  63.399  1.00 30.00           C
ATOM   6240  C   GLY B 407     -51.418  95.230  64.269  1.00 30.00           C
ATOM   6241  O   GLY B 407     -51.483  96.421  63.917  1.00 30.00           O
ATOM   6242  OXT GLY B 407     -51.993  94.809  65.273  1.00 30.00           O

AND a few more doubts—

  1. My protein contains SAM ligand. toppar_c36_jul21 does not contain prm and rtf files but the gromacs usable charmm36 ff contains parameters and topology (rtp). If I want to build my system using CHARMM-GUI, I have to provide SAM prm and rtf files. I there a way to convert SAM rtp to charmm format prm and rtf files.
  2. I want to build my simulation system using gromcas’ pdb2gmx with charmm36m ff and convert (using parmed) to Amber parm7 and rst7 to run simulations in Amber engine. Do I have to make any changes (or precautions) for the above protocol.

Please help me resolve this problem.

Thank you,
Venkat

2

Hi Venkat,

As for your first problem, it is probably the same as this one: Newest CHARMM36 port for GROMACS - #8 by Leonardo. It is a bug in the GROMACS port of the CHARMM36 FF, where the C-terminus entry has been incorrectly constructed. It will be fixed in the next release. Until then, please apply the manual fix in the thread above.

As for your other questions:

  1. the SAM ligand is implemented in the upstream CHARMM data set (topar_c36_jul21) as a patch residue, which can be applied onto ADE (in the stream file stream/prot/toppar_all36_prot_na_combined.str). As GROMACS does not have such a flexible patching facility, the porting script simply creates the already patched topology in the .rtp file. I’m not sure if CHARMM-GUI can handle patch residues or not, but if you build a molecular model for your ligand (by PyMOL or any 3D chemical builder program) and label the atoms according the topology, you can construct the topology for it by pdb2gmx and combine this and that of your system.
  2. I’m not an expert in Amber, but if your topology is complete and correct in GROMACS (the topol.top file includes all molecule topologies and the corresponding interaction parameters), then the Amber tools should also make a correct topology.

I hope this helps.

Kind regards,
Andras

1 Like
3

Dear Awacha,

Thank you very much for your answer.
It worked and I could build topol.top file now.

Regards,
Venkat