[AMBER] issues with non-bonded and bonded force field parameterisation for Arsenic

From: Dr. Srinivasa B. Ramisetti <ramisetti.serc.res.in>
Date: Thu, 17 Jun 2021 11:15:06 +0530


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


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


-----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 (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

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,

line 1909, in gene_model_files

build_large_model(mol, reslist, lmsresids, lmsresace, lmsresnme, lmsresgly,

line 1603, in build_large_model

write_gau_mkf(outf, gmkf, lgchg, SpinNum, gatms, ionnames,

line 286, in write_gau_mkf

chg = int(round(chargedict[ionname], 0))

KeyError: 'P'

Thank you,


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Received on Wed Jun 16 2021 - 23:00:03 PDT
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