Look for crystallographic data and atomic/ionic/VdW radii databases.1.05
was the ratio between Se and S vdw radii..
Il 03/dic/2017 11:59, "minyuan.mail.ustc.edu.cn" <minyuan.mail.ustc.edu.cn>
ha scritto:
Thank you!
I'll have a try.
" multiplying sigma by 1.05"
How to decide the value of 1.05?
minyuan.mail.ustc.edu.cn
From: Lorenzo Gontrani
Date: 2017-12-03 18:49
To: AMBER Mailing List
Subject: Re: [AMBER] MCPB.py to generate force field parameter for metal
ion As3+
You can use the atom types of phosphorus tetracoordinated and scale
purposely the vdw radii (sigma of LJ).I have done it succesfully for
selenium,using the sulphur s6 atom type,and multiplying sigma by 1.05 (if I
remember well, I am not at work now),and I put the bond stretching and
angle bending equilibrium values I had calculated ab initio with
Gaussian.The wesults were surprisingly accurate!
Il 03/dic/2017 11:35, "minyuan.mail.ustc.edu.cn" <minyuan.mail.ustc.edu.cn>
ha scritto:
> 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 - 03:30:02 PST
