Hi all,
Recently, I have been trying to derive the force field parameters for As3+ ion (non-bonded parameters) and H3AsO4 molecule (bonded parameters). I have seen similar queries in this mailing list but unfortunately, they weren’t quite helpful in resolving my problem even after following the suggestions. So, I would like to request for your support in deriving the force field parameters for the above two cases.
1) For a single As3+ ion, I created the As.pdb with AS and ARS as the atom and residue name. Then, I generated the As. mol2 file by using metalpdb2mol2.py -i As.pdb -o As.mol2 -c 3. Following the instructions in the 12-6 LJ non-bonded example for Zn ion, I have adapted the tleap input for As3+ ion. See below the input file.
tleap -s -f As_test.in > As_test.out
-----As_test.in-------
source leaprc.protein.ff14SB
source leaprc.gaff
source leaprc.water.tip3p
loadoff ARS.lib
mol = loadpdb As.pdb
savepdb mol As_Sys.pdb
saveamberparm mol As_Sys.prmtop As_Sys.inpcrd
quit
-----End of As_test.in------
On running the command (tleap -s -f As_test.in > As_test.out), I get one error which says “For atom (.R<ARS 1>.A<AS 1>) could not find vdW (or other) parameters for type (As3+)”. How do I fix this problem? As an alternative solution, Can I use the UFF force field parameters for As3+ ions as tleap also picks these parameters from UFF?
2) For the Arsenic acid (H3AsO4), I replaced As with P as suggested in the mailing list and generated the mol2 file using antechamber without any issues. Executing the command (MCPB.py -i H3AsO4.in -s 1) led to an error (see below) in gauio.py file. How can I resolve this issue?
Traceback (most recent call last):
File "/soft/opensoft/amber20_src/bin/MCPB.py", line 651, in <module>
gene_model_files(orpdbf, ionids, addres, addbpairs, gname, ff_choice,
File "/soft/opensoft/amber20_src/lib/python3.8/site-packages/pymsmt/mcpb/gene_model_files.py", line 1909, in gene_model_files
build_large_model(mol, reslist, lmsresids, lmsresace, lmsresnme, lmsresgly,
File "/soft/opensoft/amber20_src/lib/python3.8/site-packages/pymsmt/mcpb/gene_model_files.py", line 1603, in build_large_model
write_gau_mkf(outf, gmkf, lgchg, SpinNum, gatms, ionnames,
File "/soft/opensoft/amber20_src/lib/python3.8/site-packages/pymsmt/mol/gauio.py", line 286, in write_gau_mkf
chg = int(round(chargedict[ionname], 0))
KeyError: 'P'
Thank you,
Srinivasa
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jun 17 2021 - 08:00:02 PDT
