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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Received on Mon Dec 04 2017 - 22:30:03 PST
