Hi Srinivasa,
> On Jun 17, 2021, at 12:45 AM, Dr. Srinivasa B. Ramisetti <ramisetti.serc.res.in> wrote:
>
> Hi,
>
> Recently, I have been trying to derive the force field parameters for As3+ ion (non-bonded parameters) and H_3 AsO4 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?
You need to load a frcmod file for the As3+ ion.
> As an alternative solution, Can I use the UFF force field parameters for As3+ ions as tleap also picks these parameters from UFF?
>
MCPB.py adopted the 12-6 parameters for As3+ from the UFF paper (Rappe et al. JACS, 114, 10024). You can use it for the bonded model of ion (especially when the ion is in a buried site), but its accuracy for using in the nonbonded model of ion is not guaranteed.
> 2)For the Arsenic acid (H_3 AsO_4 ), 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 H_3 AsO_4 .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'
>
I guess this error means MCPB.py could not recognize the ion in this case (P is not an ion). You need to make sure the PDB file and mol2 file are compatible with each other, and in both of them the residue name ARS and atom name AS should be used for the As ion in order for MCPB.py to recognize the As ion.
Pengfei
> Thank you,
>
> Srinivasa
>
>
>
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Received on Thu Jun 17 2021 - 15:30:02 PDT
