Hi,
In your system, the iron sulfur cluster is not biomacromolecule, which maybe should apply GAFF force field. Adding 'gaff 2' (2 means using GAFF2) in your input file may solve this problem.
________________________________
发件人: Kaleem Arshad via AMBER <amber.ambermd.org>
发送时间: 2023年12月5日 11:15
收件人: AMBER Mailing List <amber.ambermd.org>
主题: [AMBER] MCPC.py Iron Sulfur Cluster Parameterization Issus
Hi, AMBER Users, I am trying to generate modeling files for a mycobacterial protein containing an iron sulfur cluster. But I am facing issue that my command generates all files (small, standard, and large) except large_mk input file. Below is the shown message and my input file, Iron, and Sulfur mol2 files. Any help in this regard will be greatly appreciated.
Totally there are 81 atoms in the large model.
Totally there are 490 electrons in the large model.
Traceback (most recent call last):
File "/opt/amber22/bin/MCPB.py", line 651, in <module>
gene_model_files(orpdbf, ionids, addres, addbpairs, gname, ff_choice,
File "/opt/amber22/lib/python3.11/site-packages/pymsmt/mcpb/gene_model_files.py", line 1909, in gene_model_files
build_large_model(mol, reslist, lmsresids, lmsresace, lmsresnme, lmsresgly,
File "/opt/amber22/lib/python3.11/site-packages/pymsmt/mcpb/gene_model_files.py", line 1603, in build_large_model
write_gau_mkf(outf, gmkf, lgchg, SpinNum, gatms, ionnames,
File "/opt/amber22/lib/python3.11/site-packages/pymsmt/mol/gauio.py", line 312, in write_gau_mkf
raise pymsmtError("Could not find VDW parameters/radius for "
pymsmt.exp.pymsmtError: Could not find VDW parameters/radius for element S with charge +-2
software_version gms
ion_ids 13432 13433 13434 13435 13436 13437 13438 13439
ion_mol2files F.mol2 S.mol2
original_pdb etfd_final.pdb
cut_off 2.8
force_field ff19SB
group_name etfd
large_opt 1
.<TRIPOS>MOLECULE
S
1 0 1 0 0
SMALL
User Assigned Charge
.<TRIPOS>ATOM
13436 S 4.3400 4.3650 -5.5750 S 887 S -2.000000
13437 S 4.5150 5.3110 -8.3530 S 888 S -2.000000
13438 S 2.6920 6.6530 -6.5760 S 889 S -2.000000
13439 S 5.6200 6.9320 -6.1650 S 890 S -2.000000
.<TRIPOS>BOND
.<TRIPOS>SUBSTRUCTURE
1 S 1 TEMP 0 **** **** 0 ROOT
.<TRIPOS>MOLECULE
FE
1 0 1 0 0
SMALL
User Assigned Charge
.<TRIPOS>ATOM
13432 FE 4.3070 7.3550 -7.7790 FE 883 FE 2.000000
13433 FE 3.9910 6.3520 -4.9120 FE 884 FE 2.000000
13434 FE 5.9580 4.9380 -6.8300 FE 885 FE 2.000000
13435 FE 2.9270 4.6190 -7.1210 FE 886 FE 2.000000
.<TRIPOS>BOND
.<TRIPOS>SUBSTRUCTURE
1 FE 1 TEMP 0 **** **** 0 ROOT
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Dec 05 2023 - 01:30:04 PST
