Re: [AMBER] to generate force field parameter for metal ion As3+

From: Lorenzo Gontrani <>
Date: Sun, 3 Dec 2017 11:19:42 +0100

You can use phosphorus parameters and tune LennardJones,as a first
it a free ion or bonded?

Il 03/dic/2017 04:49, "MinYuan" <> ha scritto:


I tried to use 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

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.

Yuan Min
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Received on Sun Dec 03 2017 - 02:30:03 PST
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