Thank you.
It is a bonded molecule As(OH)3. And I'm trying to use MCPB.py bonded model.
In MCPB.py reference, arsenic is included as one of 80 metals supported by MCPB.py.
http://pubs.acs.org/doi/abs/10.1021/acs.jcim.5b00674
Before using MCPB.py, one need first generate a mol2 file using antechamber.
The result mol2 file indicates, antechamber cannot recognize arsenic and name it as a "DU" atom in mol2 file.
minyuan.mail.ustc.edu.cn
From: Lorenzo Gontrani
Date: 2017-12-03 18:19
To: AMBER Mailing List
Subject: Re: [AMBER] MCPB.py to generate force field parameter for metal ion As3+
You can use phosphorus parameters and tune LennardJones,as a first try..is
it a free ion or bonded?
Il 03/dic/2017 04:49, "MinYuan" <minyuan.mail.ustc.edu.cn> ha scritto:
Hi,
I tried to use MCPB.py to generate force field parameter for metal ion As3+
My input file is ARS.pdb, which contains:
ATOM 1 AS ARS 1 -0.315 0.310 0.441 1.00 0.00
As
However, to generate mol2 file, using command:
antechamber -fi pdb -fo mol2 -i ARS.pdb -o ARS.mol2 -pf y
Information comes with WARNING:
-------------------------------------------------------------
$ antechamber -fi pdb -fo mol2 -i ARS.pdb -o ARS.mol2 -pf y
Welcome to antechamber 17.3: molecular input file processor.
acdoctor mode is on: check and diagnosis problems in the input file.
-- Check Format for pdb File --
Status: pass
-- Check Unusual Elements --
Warning: Unusual element () for atom (ID: 1, Name: AS).
GAFF does not have sufficient parameters for molecules having unusual
elements (those other than H,C,N,O,S,P and halogens).
To ensure antechamber works properly, one may need to designate
bond types for bonds involved with unusual elements.
To do so, simply freeze the bond types by appending "F" or "f"
to the corresponding bond types in ac or mol2 files.
-- Check Open Valences --
Warning: This molecule has no hydrogens nor halogens.
It is quite possible that there are unfilled valences.
-- Check Geometry --
for those bonded
for those not bonded
Status: pass
-- Check Weird Bonds --
Status: pass
-- Check Number of Units --
Status: pass
acdoctor mode has completed checking the input file.
-----------------------------------------------------------------------
If it is impossible to generate mol2 of As with antechamber,
what can I do with it alternatively?
Looking forward to hear your reply soon.
Best,
Yuan Min
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Received on Sun Dec 03 2017 - 03:00:02 PST
