Thank you for your reply!
It works!
Using pop=mkuff can fix the problem and there is no need to use script fixreadinesp.sh.
> -----原始邮件-----
> 发件人: "Lorenzo Gontrani" <lorenzo.gontrani.gmail.com>
> 发送时间: 2017-12-05 14:17:54 (星期二)
> 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+
>
> Use pop=mkuff G09 doesn't have all MK radii
>
> Il 05/dic/2017 03:12, "MinYuan" <minyuan.mail.ustc.edu.cn> ha scritto:
>
> It may be the gaussian 09 bug on dealing with MK RESP charge calculations.
>
>
> > -----原始邮件-----
> > 发件人: MinYuan <minyuan.mail.ustc.edu.cn>
> > 发送时间: 2017-12-05 10:09:03 (星期二)
> > 收件人: "AMBER Mailing List" <amber.ambermd.org>
> > 抄送:
> > 主题: Re: Re: [AMBER] MCPB.py to generate force field parameter for metal
> ion As3+
> >
> > Hi Li,
> >
> > Thank you for your reply!
> >
> > I modified the mol2 file of AS and typed command: $ MCPB.py -i COMPLEX.in
> -s 1
> > Everything went well until the large model:
> > ------------------------------------------------------------
> -----------------------
> > Traceback (most recent call last):
> > File "/home/miny/amber/amber16/bin/MCPB.py", line 644, in <module>
> > addred, lgchg, lgspin)
> > File "/home/miny/amber/amber16/lib/python2.7/site-packages/
> pymsmt/mcpb/gene_model_files.py", line 1901, in gene_model_files
> > ionids, chargedict, lgchg, lgspin, outf, watermodel, largeopt, sqmopt)
> > File "/home/miny/amber/amber16/lib/python2.7/site-packages/
> pymsmt/mcpb/gene_model_files.py", line 1596, in build_large_model
> > chargedict, IonLJParaDict, largeopt)
> > File "/home/miny/amber/amber16/lib/python2.7/site-packages/pymsmt/mol/gauio.py",
> line 294, in write_gau_mkf
> > chg = int(round(chargedict[ionname], 0))
> > KeyError: 'AS'
> > ------------------------------------------------------------
> ----------------------
> >
> > I performed small model geometry optimization, then force constant
> calculation, and all went well.
> > But, when tried to employ MK RESP charge calculation: g09 <
> COMPLEX_large_mk.com > COMPLEX_large_mk.log
> > g09 terminated with an error and in its log file:
> >
> > ------------------------------------------------------------
> ---------------------
> >
> > No NMR shielding tensors so no spin-rotation constants.
> > Leave Link 601 at Tue Dec 5 09:51:32 2017, MaxMem= 3932160000 cpu:
> 0.4
> > FitSet: NAtFit= 7 NAtPot= 7 NAtFrz= 0 MDM= 11 TotChg=
> 0.00000
> > Merz-Kollman atomic radii used.
> > Read replacement radii for each type of atom:
> > Atom Element Radius
> > 1 8 1.40
> > 2 1 1.20
> > 3 8 1.40
> > 4 1 1.20
> > 5 8 1.40
> > 6 1 1.20
> > 7 33 0.00
> > GetVDW: no radius for atom 7 atomic number 33.
> > Error termination via Lnk1e in /opt/g09/l602.exe at Tue Dec 5 09:51:32
> 2017.
> > Job cpu time: 0 days 0 hours 0 minutes 14.2 seconds.
> > -----------------------------------------------------------------------
> >
> >
> > Is it normal?
> > Sorry for bothering you.
> > Looking forward to hear your help!
> >
> > Best wishes
> > Yuan Min
> >
> >
> > > -----原始邮件-----
> > > 发件人: "Pengfei Li" <ambermailpengfei.gmail.com>
> > > 发送时间: 2017-12-05 06:07:12 (星期二)
> > > 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+
> > >
> > > Hi Yuan,
> > >
> > > If Antechamber can not give a mol2 file you like, you can manually
> change the content inside it. For example, You can manually change the “DU”
> atom type to “AS”, and the charge of it to 3.00.
> > >
> > > Kind regards,
> > > Pengfei
> > >
> > > > On Dec 3, 2017, at 5:57 AM, MinYuan <minyuan.mail.ustc.edu.cn> wrote:
> > > >
> > > > 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
> > > >>> _______________________________________________
> > > >>> AMBER mailing list
> > > >>> AMBER.ambermd.org
> > > >>> http://lists.ambermd.org/mailman/listinfo/amber
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> > > >>>
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Received on Tue Dec 05 2017 - 04:00:03 PST
