Hi everyone,
I'm trying to use MCPB.py to obtain parameters for Cyhexatin monovalent cation (Sn atom bound to three cyclohexane rings). In my pdb structure file, Sn - C bond lengths range from 2.18 - 2.21 A.
I ran first command in MCPB protocol (MCPB.py -i Cyhexatin.in -s 1) and I realized that one of ligands are not reading by the program (information below).
Someone have some hint to overcome this issue?
I processed the files in different ways and I always face this same problem. I can go further and finish all steps, but it's very obvious that the final parameters are not correct.
Below the MCPB information about metal site skipping the residue number 3. After this information, my input file for the first step of MCPB.py.
Thanks in advance,
Fred
******************************************************************
* *
*=======================Metal Site Information===================*
* *
******************************************************************
***Selected Metal ion SN is atom 1 in residue 1-SN
2-CYL.C is in 2.6 Angstrom of or set bonded (in the input file) to (one of) these metal ions
4-CYL.C is in 2.6 Angstrom of or set bonded (in the input file) to (one of) these metal ions
***The following residues are in the Metal Site:
Residue 1-SN
Residue 2-CYL
Residue 4-CYL
***The small model contains the following residues:
[1, 2, 4]
***The large model contains the following residues:
[1, 2, 4]
******************************************************************
Cyhexatin.in file:
original_pdb Cyhexatin_cation.pdb
group_name Cyhexatin
cut_off 2.6
ion_ids 1
large_opt 1
lgmodel_chg 1
lgmodel_spin 1
add_bonded_pairs 1-5
add_bonded pairs 1-19
add_bonded_pairs 1-36
force_field ff19SB
software_version g16
ion_mol2files Cyhexatin_SN.mol2
naa_mol2files CYL.mol2
frcmod_files CYL.frcmod
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Received on Mon May 22 2023 - 16:00:03 PDT
