Thank you for your reply.
> -----原始邮件-----
> 发件人: "Lorenzo Gontrani" <lorenzo.gontrani.gmail.com>
> 发送时间: 2017-12-03 19:10:43 (星期日)
> 收件人: "AMBER Mailing List" <amber.ambermd.org>
> 抄送:
> 主题: Re: [AMBER] MCPB.py to generate force field parameter for metal ion As3+
>
> 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 - 04:00:02 PST
