Demir,Thank you for your help.
I create a template file like this according to your suggestion:
#P B3LYP/6-31G* SCF=(Conver=8,xqc) maxcyc=500
and modified the parameter ".in" file in the $gau part as follows:
......
&gau
method = 'B3LYP',
basis = '6-31G*',
num_threads = 10,
mem = '6GB'
use_template = 1,
&end
But it don't wokrs, what should I do?
Tianyou XIn
> -----Original Messages-----
> From: amber-request.ambermd.org
> Sent Time: 2020-03-06 04:00:01 (Friday)
> To: amber.ambermd.org
> Cc:
> Subject: AMBER Digest, Vol 2932, Issue 1
>
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> AMBER Mailing List Digest
>
> Today's Topics:
>
> 1. Re: adding Na, K and Cl ions matching intracellular conc
> (Matias Machado)
> 2. Re: adding Na, K and Cl ions matching intracellular conc
> (Matias Machado)
> 3. problem in MCPB.py (wujue)
> 4. Re: adding Na, K and Cl ions matching intracellular conc
> (Vaibhav Dixit)
> 5. Re: Citing DNA OL15 forcefield (Sruthi Sudhakar)
> 6. QM/MM Convergence questions (???)
> 7. Re: QM/MM Convergence questions (Busra Demir)
> 8. error job.sh (MYRIAN TORRES RICO)
> 9. Re: error job.sh (Gustaf Olsson)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 04 Mar 2020 21:23:01 -0300 (UYT)
> From: Matias Machado <mmachado.pasteur.edu.uy>
> Subject: Re: [AMBER] adding Na, K and Cl ions matching intracellular
> conc
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <f41330f9-2999-4616-b37f-585b10e0386d.free.ipmont.lan>
> Content-Type: text/plain; charset=utf-8
>
> Dear Vaibhav,
>
> I recommend you to use the SPLIT method, which is described here:
>
> Split the Charge Difference in Two! A Rule of Thumb for Adding Proper Amounts of Ions in MD Simulations
> [https://doi.org/10.1021/acs.jctc.9b00953]
>
> The keyword "saltcon" has nothing to do in explicit solvent MDs.
>
> Best regards,
>
> Matias Machado
>
> ------------------------------------
> PhD.
> Researcher at Biomolecular Simulations Lab.
> Institut Pasteur de Montevideo | Uruguay
> [http://pasteur.uy/en/labs/biomolecular-simulations-laboratory]
> [http://www.sirahff.com]
>
> ----- Mensaje original -----
> De: "Vaibhav Dixit" <vaibhavadixit.gmail.com>
> Para: "AMBER Mailing List" <amber.ambermd.org>
> Enviados: Mi?rcoles, 4 de Marzo 2020 9:49:40
> Asunto: [AMBER] adding Na, K and Cl ions matching intracellular conc
>
> Dear All,
> I'm interested in understanding if/which Na, K and Cl ions explicitly enter
> into the active site of a given protein during MD simulation.
> But I can't find a way/trick (from the manual or older posts) to add all
> these ions matching the intracellular concentrations and while keeping the
> system neutral.
> I'm guessing someone in the list must have already done a similar thing.
> Thus can someone please suggest me on this aspect.
> I'm assuming that if this can be done then I'll have to use saltcon=0 to
> avoid GB modelling for salt concentrations.
> Looking forward to receiving valuable suggestions from the list.
>
> Thank you and best regards.
> Vaibhav
>
>
> --
>
> Regards,
>
> Dr. Vaibhav A. Dixit,
>
> Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The
> University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
> AND
> Assistant Professor,
> Department of Pharmacy,
> ?????????????????????????????????????????????
> Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
> VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
> India.
> Phone No. +91 1596 255652, Mob. No. +91-7709129400,
> Email: vaibhav.dixit.pilani.bits-pilani.ac.in, vaibhavadixit.gmail.com
> http://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile
> https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
>
> ORCID ID: https://orcid.org/0000-0003-4015-2941
>
> http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
>
> P Please consider the environment before printing this e-mail
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 04 Mar 2020 21:24:40 -0300 (UYT)
> From: Matias Machado <mmachado.pasteur.edu.uy>
> Subject: Re: [AMBER] adding Na, K and Cl ions matching intracellular
> conc
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <7587d6cc-4ee3-4888-8a39-b92ecd43a914.free.ipmont.lan>
> Content-Type: text/plain; charset=utf-8
>
> you can also check this previous post:
>
> [http://archive.ambermd.org/202002/0194.html]
>
> Best,
>
> Matias
>
> ----- Mensaje original -----
> De: "Matias Machado" <mmachado.pasteur.edu.uy>
> Para: "AMBER Mailing List" <amber.ambermd.org>
> Enviados: Mi?rcoles, 4 de Marzo 2020 21:23:01
> Asunto: Re: [AMBER] adding Na, K and Cl ions matching intracellular conc
>
> Dear Vaibhav,
>
> I recommend you to use the SPLIT method, which is described here:
>
> Split the Charge Difference in Two! A Rule of Thumb for Adding Proper Amounts of Ions in MD Simulations
> [https://doi.org/10.1021/acs.jctc.9b00953]
>
> The keyword "saltcon" has nothing to do in explicit solvent MDs.
>
> Best regards,
>
> Matias Machado
>
> ------------------------------------
> PhD.
> Researcher at Biomolecular Simulations Lab.
> Institut Pasteur de Montevideo | Uruguay
> [http://pasteur.uy/en/labs/biomolecular-simulations-laboratory]
> [http://www.sirahff.com]
>
> ----- Mensaje original -----
> De: "Vaibhav Dixit" <vaibhavadixit.gmail.com>
> Para: "AMBER Mailing List" <amber.ambermd.org>
> Enviados: Mi?rcoles, 4 de Marzo 2020 9:49:40
> Asunto: [AMBER] adding Na, K and Cl ions matching intracellular conc
>
> Dear All,
> I'm interested in understanding if/which Na, K and Cl ions explicitly enter
> into the active site of a given protein during MD simulation.
> But I can't find a way/trick (from the manual or older posts) to add all
> these ions matching the intracellular concentrations and while keeping the
> system neutral.
> I'm guessing someone in the list must have already done a similar thing.
> Thus can someone please suggest me on this aspect.
> I'm assuming that if this can be done then I'll have to use saltcon=0 to
> avoid GB modelling for salt concentrations.
> Looking forward to receiving valuable suggestions from the list.
>
> Thank you and best regards.
> Vaibhav
>
>
> --
>
> Regards,
>
> Dr. Vaibhav A. Dixit,
>
> Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The
> University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
> AND
> Assistant Professor,
> Department of Pharmacy,
> ?????????????????????????????????????????????
> Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
> VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
> India.
> Phone No. +91 1596 255652, Mob. No. +91-7709129400,
> Email: vaibhav.dixit.pilani.bits-pilani.ac.in, vaibhavadixit.gmail.com
> http://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile
> https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
>
> ORCID ID: https://orcid.org/0000-0003-4015-2941
>
> http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
>
> P Please consider the environment before printing this e-mail
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> ------------------------------
>
> Message: 3
> Date: Thu, 5 Mar 2020 11:41:49 +0800 (CST)
> From: wujue <wuj18650693661.163.com>
> Subject: [AMBER] problem in MCPB.py
> To: "amber.ambermd.org" <amber.ambermd.org>
> Message-ID:
> <50ad3f2f.3358.170a8c8feb0.Coremail.wuj18650693661.163.com>
> Content-Type: text/plain; charset=GBK
>
> Distinguished Sir or Madam
>
> I'm trying to use MCPB.py for performing parameterizations for both the metalloprotein and organometallic compound systems. I followed the steps to prepare the PDB and mol2 files for the non-standard residues and metal ions in the tutorial and there was errors in the first step of generating the PDB, Gaussian and fingerprint modeling files.
>
> Here are my error messages:
>
> *****************************************************************
>
> * *
>
> *=======================Metal Site Information===================*
>
> * *
>
> ******************************************************************
>
> ***Selected Metal ion NI is atom 37834 in residue 2476-NI1
>
> 146-GLN.OE1 is in 2.8 Angstrom of or set bonded (in the input file) to (one of) these metal ions
>
> 2475-F31.NA is in 2.8 Angstrom of or set bonded (in the input file) to (one of) these metal ions
>
> 2475-F31.NB is in 2.8 Angstrom of or set bonded (in the input file) to (one of) these metal ions
>
> 2475-F31.NC is in 2.8 Angstrom of or set bonded (in the input file) to (one of) these metal ions
>
> 2475-F31.ND is in 2.8 Angstrom of or set bonded (in the input file) to (one of) these metal ions
>
> ***The following residues are in the Metal Site:
>
> Residue 146-GLN
>
> Residue 2475-F31
>
> Residue 2476-NI1
>
> ***The small model contains the following residues:
>
> [146, 2475, 2476]
>
> ***The large model contains the following residues:
>
> [145, 146, 147, 2475, 2476]
>
> ******************************************************************
>
> * *
>
> *=======================Building models==========================*
>
> * *
>
> ******************************************************************
>
> ***Creating the small model...
>
> It contains the residue 146-GLN as sidechain coordinated.
>
> It contains the residue 2475-F31 as normal.
>
> It contains the residue 2476-NI1 as normal.
>
> Totally there are 125 atoms in the small model.
>
> Traceback (most recent call last):
>
> File "/usr/local/theochem/amber16/amber16/bin/MCPB.py", line 644, in <module>
>
> addred, lgchg, lgspin)
>
> File "/usr/local/theochem/amber16/amber16/lib/python2.7/site-packages/pymsmt/mcpb/gene_model_files.py", line 1895, in gene_model_files
>
> smspin, addred, outf, sqmopt)
>
> File "/usr/local/theochem/amber16/amber16/lib/python2.7/site-packages/pymsmt/mcpb/gene_model_files.py", line 1380, in build_small_model
>
> AtNum = Atnum[gatm.element]
>
> KeyError: '2'
>
> This problem confused me. I tried to rebuild the model and repeat the preparations in the tutorials. It seems to be that the number of electrons in the model is wrong. But I don't know how to solve it.
>
> Could someone help me out of the problem? Any response will be highly appreciated!
> Yours,
> Wu Jue
>
> ------------------------------
>
> Message: 4
> Date: Thu, 5 Mar 2020 09:49:41 +0530
> From: Vaibhav Dixit <vaibhavadixit.gmail.com>
> Subject: Re: [AMBER] adding Na, K and Cl ions matching intracellular
> conc
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAO6-0TnVyke691viB-oxWGTsgsMo0dL0tm5KWL=R_N4B+2LZZQ.mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Dear Matias and Amber list,
> Thanks for the interesting suggestions and reference (I'll read it in
> detail soon).
> Just wondering if one can generalize this to dividing the charge by n,
> where n is the total number of unique ions.
> E.g. divide by 3 in case we want a combination of NaCl (2.5 mM) and KCl
> (140 mM) at their typical intracellular concentrations.
> Using this one can then simulate situations where intracellular Ca ions
> increases 10-1000 fold (here we will divide by 5 to account for NaCl, KCl
> and CaCl2).
>
> Please let me know your thoughts and if this approach is meaningful.
> Thank you.
>
> On Thu, Mar 5, 2020 at 5:55 AM Matias Machado <mmachado.pasteur.edu.uy>
> wrote:
>
> > you can also check this previous post:
> >
> > [http://archive.ambermd.org/202002/0194.html]
> >
> > Best,
> >
> > Matias
> >
> > ----- Mensaje original -----
> > De: "Matias Machado" <mmachado.pasteur.edu.uy>
> > Para: "AMBER Mailing List" <amber.ambermd.org>
> > Enviados: Mi?rcoles, 4 de Marzo 2020 21:23:01
> > Asunto: Re: [AMBER] adding Na, K and Cl ions matching intracellular conc
> >
> > Dear Vaibhav,
> >
> > I recommend you to use the SPLIT method, which is described here:
> >
> > Split the Charge Difference in Two! A Rule of Thumb for Adding Proper
> > Amounts of Ions in MD Simulations
> > [https://doi.org/10.1021/acs.jctc.9b00953]
> >
> > The keyword "saltcon" has nothing to do in explicit solvent MDs.
> >
> > Best regards,
> >
> > Matias Machado
> >
> > ------------------------------------
> > PhD.
> > Researcher at Biomolecular Simulations Lab.
> > Institut Pasteur de Montevideo | Uruguay
> > [http://pasteur.uy/en/labs/biomolecular-simulations-laboratory]
> > [http://www.sirahff.com]
> >
> > ----- Mensaje original -----
> > De: "Vaibhav Dixit" <vaibhavadixit.gmail.com>
> > Para: "AMBER Mailing List" <amber.ambermd.org>
> > Enviados: Mi?rcoles, 4 de Marzo 2020 9:49:40
> > Asunto: [AMBER] adding Na, K and Cl ions matching intracellular conc
> >
> > Dear All,
> > I'm interested in understanding if/which Na, K and Cl ions explicitly enter
> > into the active site of a given protein during MD simulation.
> > But I can't find a way/trick (from the manual or older posts) to add all
> > these ions matching the intracellular concentrations and while keeping the
> > system neutral.
> > I'm guessing someone in the list must have already done a similar thing.
> > Thus can someone please suggest me on this aspect.
> > I'm assuming that if this can be done then I'll have to use saltcon=0 to
> > avoid GB modelling for salt concentrations.
> > Looking forward to receiving valuable suggestions from the list.
> >
> > Thank you and best regards.
> > Vaibhav
> >
> >
> > --
> >
> > Regards,
> >
> > Dr. Vaibhav A. Dixit,
> >
> > Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The
> > University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
> > AND
> > Assistant Professor,
> > Department of Pharmacy,
> > ?????????????????????????????????????????????
> > Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
> > VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
> > India.
> > Phone No. +91 1596 255652, Mob. No. +91-7709129400,
> > Email: vaibhav.dixit.pilani.bits-pilani.ac.in, vaibhavadixit.gmail.com
> > http://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile
> > https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
> >
> > ORCID ID: https://orcid.org/0000-0003-4015-2941
> >
> > http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
> >
> > P Please consider the environment before printing this e-mail
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> --
>
> Regards,
>
> Dr. Vaibhav A. Dixit,
>
> Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The
> University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
> AND
> Assistant Professor,
> Department of Pharmacy,
> ?????????????????????????????????????????????
> Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
> VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
> India.
> Phone No. +91 1596 255652, Mob. No. +91-7709129400,
> Email: vaibhav.dixit.pilani.bits-pilani.ac.in, vaibhavadixit.gmail.com
> ?http://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile
> https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
>
> ORCID ID: https://orcid.org/0000-0003-4015-2941
>
> http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
>
> P Please consider the environment before printing this e-mail
>
>
> ------------------------------
>
> Message: 5
> Date: Thu, 5 Mar 2020 14:30:18 +0530
> From: Sruthi Sudhakar <sruthisudhakarraji.gmail.com>
> Subject: Re: [AMBER] Citing DNA OL15 forcefield
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAG8eZXyUWNhVHcifM0P_j1NuhC0q9zjp-UVvVVJx20oHErgp7Q.mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Just to be sure, these references were given in the manual. Should we
> include these as well?
>
>
> Krepl, M.; Zgarbova, M.; Stadlbauer, P.; Otyepka, M.; Banas, P.; Koca, J.;
> Cheatham, T.E. III; Sponer, J. Reference simulations of noncanonical
> nucleic acids with different chi variants of the AMBER force ?eld:
> Quadruplex DNA, quadruplex RNA, and Z-DNA. J. Chem. Theory Comp.,2012, 8,
> 2506?2520
>
> Zgarbov?, Marie; Luque, F. Javier; ?poner, Ji?ri; III, Thomas E. Cheatham;
> Otyepka, Michal; Jure?cka, Petr. Toward improved description of dna
> backbone: Revisiting epsilon and zeta torsion force ?eld parameters. J.
> Chem. Theory Comput.,2013, 9, 2339?2354.
>
> Zgarbov?, M.; Sponer, J.; Otyepka, M.; Cheatham, T.E. III;
> Galindo-Murillo, R.; Jure?cka, P. Re?nement of the Sugar-Phosphate Backbone
> Torsion Beta for AMBER Force Fields Improves the Description of Z- and
> B-DNA. J. Chem. Theor. and Comp.,2015, 12, 5723?5736
>
> On Thu, Mar 5, 2020 at 1:25 AM Christina Bergonzo <cbergonzo.gmail.com>
> wrote:
>
> > This info can be found at the top of the leaprc.DNA.OL15 file:
> >
> > # Uses ff99bsc0+OL15 for DNA
> > # (ff99): Wang et al. J. Comp. Chem. 21: 1049, 2000
> > # (bsc0): Perez et al. Biophys J. 92: 3817, 2007
> > # (OL15): Zgarbova et al. JCTC 11: 5723, 2015
> >
> > On Wed, Mar 4, 2020 at 2:15 PM Sruthi Sudhakar <
> > sruthisudhakarraji.gmail.com>
> > wrote:
> >
> > > Respected group members,
> > > Could anyone tell me how to cite the DNAOL15 forcefield in our papers? I
> > > have read about how to cite the other force fields, except this one.
> > > Thanking you in advance.
> > >
> > > Sruthi
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> > --
> > -----------------------------------------------------------------
> > Christina Bergonzo
> > Research Chemist
> > Biomolecular Measurement Division, MML, NIST
> > -----------------------------------------------------------------
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> ------------------------------
>
> Message: 6
> Date: Thu, 5 Mar 2020 17:07:44 +0800 (GMT+08:00)
> From: ??? <xzhfood.njau.edu.cn>
> Subject: [AMBER] QM/MM Convergence questions
> To: amber.ambermd.org
> Message-ID: <1d1640a7.3e1d.170a9f3613b.Coremail.xzhfood.njau.edu.cn>
> Content-Type: text/plain; charset=UTF-8
>
> Dear Amber,
>
> An error occur when I run a QM/MM with amber and gausssin09, I do not know how to solve the problems, any suggestion will be much appreciate, thank you for your help in advanced, the error information is as follows:
>
> The QM/MM input file:
>
> Initial min of our structure QMMM
> &cntrl
> imin = 1, maxcyc = 5000, ncyc=2000,
> ntb = 0,
> cut = 20.0, ntc=2, ntf=2,
> ntpr=1000,
> restraint_wt=2.0,
> ifqnt = 1
> &end
> &qmmm
> iqmatoms=1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,715,716,717,718,719,720,721,722,723,724,725,757,758,759,760,761,762,763,764,765,766,767,768,769,770,771,772,773,774,775,776,777,778,2365,2366,2367,2368,2369,2370,2371,2372,2373,2374,2375,2376,2377,2378,2379,2382,8628,8629,8630,8679,8680,8681
> qmcharge = 0,
> spin = 2,
> qm_theory = 'EXTERN',
> qmshake=1,
> qm_ewald=1, qm_pme=1,
> diag_routine=0,
> writepdb=1
> qmcut = 20.0
> &end
> &gau
> method = 'B3LYP',
> basis = '6-31G*',
> num_threads = 10,
> mem = '6GB'
> &end
>
>
> Error form the gau_job.log file,
> .....................................
> RMSDP=1.93D-04 MaxDP=3.33D-02 DE= 1.64D-04 OVMax= 8.63D-02
>
> Cycle 128 Pass 1 IDiag 1:
> RMSU= 2.75D-05 CP: 1.00D+00 -5.05D-01 -8.69D-01 2.19D+00
> E= -2424.60356615312 Delta-E= 0.001037414186 Rises=F Damp=F
> DIIS: error= 8.55D-04 at cycle 125 NSaved= 20.
> NSaved=20 IEnMin= 5 EnMin= -2424.61776698937 IErMin=19 ErrMin= 4.94D-04
> ErrMax= 8.55D-04 0.00D+00 EMaxC= 1.00D-01 BMatC= 3.31D-04 BMatP= 1.14D-04
> IDIUse=3 WtCom= 9.97D-01 WtEn= 2.98D-03
> Rare condition: small coef for last iteration: 0.000D+00
> Coeff-Com: -0.702D-01-0.293D-01-0.544D-01-0.305D+00 0.621D+00-0.423D+00
> Coeff-Com: -0.423D-01 0.140D+00 0.716D-01 0.997D-01-0.177D+00-0.897D-01
> Coeff-Com: 0.104D+00-0.256D+00 0.537D+00-0.734D+00 0.809D-01 0.274D+00
> Coeff-Com: 0.127D+01-0.203D-01
> Coeff-En: 0.000D+00 0.000D+00 0.000D+00 0.000D+00 0.000D+00 0.000D+00
> Coeff-En: 0.000D+00 0.000D+00 0.000D+00 0.000D+00 0.000D+00 0.000D+00
> Coeff-En: 0.000D+00 0.000D+00 0.000D+00 0.000D+00 0.000D+00 0.000D+00
> Coeff-En: 0.000D+00 0.100D+01
> Coeff: -0.702D-01-0.293D-01-0.544D-01-0.305D+00 0.621D+00-0.423D+00
> Coeff: -0.423D-01 0.140D+00 0.716D-01 0.997D-01-0.177D+00-0.897D-01
> Coeff: 0.104D+00-0.256D+00 0.537D+00-0.734D+00 0.809D-01 0.274D+00
> Coeff: 0.127D+01-0.203D-01
> Gap= 0.009 Goal= None Shift= 0.000
> Gap= 0.010 Goal= None Shift= 0.000
> RMSDP=6.02D-05 MaxDP=1.08D-02 DE= 1.04D-03 OVMax= 2.84D-02
>
> >>>>>>>>>> Convergence criterion not met.
> SCF Done: E(UB3LYP) = -2424.60356615 A.U. after 129 cycles
> NFock=128 Conv=0.60D-04 -V/T= 2.2388
> <Sx>= 0.0000 <Sy>= 0.0000 <Sz>= 0.5000 <S**2>= 1.5874 S= 0.8555
> <L.S>= 0.000000000000E+00
> KE= 1.957254069352D+03 PE=-1.340126621204D+04 EE= 5.052337417625D+03
> Annihilation of the first spin contaminant:
> S**2 before annihilation 1.5874, after 1.2129
> Convergence failure -- run terminated.
> Error termination via Lnk1e in /home/xzhfood/gaussian/g09/l502.exe at Thu Mar 5 03:47:42 2020.
> Job cpu time: 0 days 5 hours 47 minutes 3.7 seconds.
> File lengths (MBytes): RWF= 465 Int= 0 D2E= 0 Chk= 12 Scr= 1
>
> Tianyou Xin
>
> ------------------------------
>
> Message: 7
> Date: Thu, 5 Mar 2020 14:41:27 +0300
> From: Busra Demir <bdemir09.gmail.com>
> Subject: Re: [AMBER] QM/MM Convergence questions
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CALU0VXWXaXq9_WmREdZbNwtY5aJu2_6jL7ypZyjQTC+kohBSiA.mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Your SCF calculation didn't converge. This could be due to various reasons
> and G09 doesn't specifically say it.
> First, you should check the input parameters you choose such as charge and
> multiplicity for the calculation.
>
> If you are sure about them, there are several options but (to the best of
> my knowledge) these are the first things you could try:
> 1. try increasing number of cycles (maxcycle=xxx) in G09 input route line.
> 2. change the convergence criteria for SCF calculation (use SCF=QC instead
> of default SCF=Tight).
> 3. change convergence criteria scf_conv under &gau namelist.
>
> You can find more options about SCF calculations from gaussian website:
> https://gaussian.com/scf/
>
> Busra Demir
>
> PhD Student
> Department of Materials Science and Nanotechnology Engineering
> Bionanodesign Laboratory,
> TOBB University of Economics and Technology
> Ankara, 06560 TURKEY
>
>
>
>
> On Thu, Mar 5, 2020 at 12:07 PM ??? <xzhfood.njau.edu.cn> wrote:
>
> > Dear Amber,
> >
> > An error occur when I run a QM/MM with amber and gausssin09, I do not know
> > how to solve the problems, any suggestion will be much appreciate, thank
> > you for your help in advanced, the error information is as follows:
> >
> > The QM/MM input file:
> >
> > Initial min of our structure QMMM
> > &cntrl
> > imin = 1, maxcyc = 5000, ncyc=2000,
> > ntb = 0,
> > cut = 20.0, ntc=2, ntf=2,
> > ntpr=1000,
> > restraint_wt=2.0,
> > ifqnt = 1
> > &end
> > &qmmm
> >
> > iqmatoms=1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,715,716,717,718,719,720,721,722,723,724,725,757,758,759,760,761,762,763,764,765,766,767,768,769,770,771,772,773,774,775,776,777,778,2365,2366,2367,2368,2369,2370,2371,2372,2373,2374,2375,2376,2377,2378,2379,2382,8628,8629,8630,8679,8680,8681
> > qmcharge = 0,
> > spin = 2,
> > qm_theory = 'EXTERN',
> > qmshake=1,
> > qm_ewald=1, qm_pme=1,
> > diag_routine=0,
> > writepdb=1
> > qmcut = 20.0
> > &end
> > &gau
> > method = 'B3LYP',
> > basis = '6-31G*',
> > num_threads = 10,
> > mem = '6GB'
> > &end
> >
> >
> > Error form the gau_job.log file,
> > .....................................
> > RMSDP=1.93D-04 MaxDP=3.33D-02 DE= 1.64D-04 OVMax= 8.63D-02
> >
> > Cycle 128 Pass 1 IDiag 1:
> > RMSU= 2.75D-05 CP: 1.00D+00 -5.05D-01 -8.69D-01 2.19D+00
> > E= -2424.60356615312 Delta-E= 0.001037414186 Rises=F Damp=F
> > DIIS: error= 8.55D-04 at cycle 125 NSaved= 20.
> > NSaved=20 IEnMin= 5 EnMin= -2424.61776698937 IErMin=19 ErrMin=
> > 4.94D-04
> > ErrMax= 8.55D-04 0.00D+00 EMaxC= 1.00D-01 BMatC= 3.31D-04 BMatP= 1.14D-04
> > IDIUse=3 WtCom= 9.97D-01 WtEn= 2.98D-03
> > Rare condition: small coef for last iteration: 0.000D+00
> > Coeff-Com: -0.702D-01-0.293D-01-0.544D-01-0.305D+00 0.621D+00-0.423D+00
> > Coeff-Com: -0.423D-01 0.140D+00 0.716D-01 0.997D-01-0.177D+00-0.897D-01
> > Coeff-Com: 0.104D+00-0.256D+00 0.537D+00-0.734D+00 0.809D-01 0.274D+00
> > Coeff-Com: 0.127D+01-0.203D-01
> > Coeff-En: 0.000D+00 0.000D+00 0.000D+00 0.000D+00 0.000D+00 0.000D+00
> > Coeff-En: 0.000D+00 0.000D+00 0.000D+00 0.000D+00 0.000D+00 0.000D+00
> > Coeff-En: 0.000D+00 0.000D+00 0.000D+00 0.000D+00 0.000D+00 0.000D+00
> > Coeff-En: 0.000D+00 0.100D+01
> > Coeff: -0.702D-01-0.293D-01-0.544D-01-0.305D+00 0.621D+00-0.423D+00
> > Coeff: -0.423D-01 0.140D+00 0.716D-01 0.997D-01-0.177D+00-0.897D-01
> > Coeff: 0.104D+00-0.256D+00 0.537D+00-0.734D+00 0.809D-01 0.274D+00
> > Coeff: 0.127D+01-0.203D-01
> > Gap= 0.009 Goal= None Shift= 0.000
> > Gap= 0.010 Goal= None Shift= 0.000
> > RMSDP=6.02D-05 MaxDP=1.08D-02 DE= 1.04D-03 OVMax= 2.84D-02
> >
> > >>>>>>>>>> Convergence criterion not met.
> > SCF Done: E(UB3LYP) = -2424.60356615 A.U. after 129 cycles
> > NFock=128 Conv=0.60D-04 -V/T= 2.2388
> > <Sx>= 0.0000 <Sy>= 0.0000 <Sz>= 0.5000 <S**2>= 1.5874 S= 0.8555
> > <L.S>= 0.000000000000E+00
> > KE= 1.957254069352D+03 PE=-1.340126621204D+04 EE= 5.052337417625D+03
> > Annihilation of the first spin contaminant:
> > S**2 before annihilation 1.5874, after 1.2129
> > Convergence failure -- run terminated.
> > Error termination via Lnk1e in /home/xzhfood/gaussian/g09/l502.exe at Thu
> > Mar 5 03:47:42 2020.
> > Job cpu time: 0 days 5 hours 47 minutes 3.7 seconds.
> > File lengths (MBytes): RWF= 465 Int= 0 D2E= 0 Chk= 12
> > Scr= 1
> >
> > Tianyou Xin
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> ------------------------------
>
> Message: 8
> Date: Thu, 05 Mar 2020 18:05:40 +0100
> From: "MYRIAN TORRES RICO" <myriam.torres.iiq.csic.es>
> Subject: [AMBER] error job.sh
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <20200305180540.Horde.HupwXjZTqXFSXMx5eW1FIMT.webmail.csic.es>
> Content-Type: text/plain; charset=utf-8; format=flowed; DelSp=Yes
>
>
> Hi all,
>
> When I launch my script, this error appears:
>
> | APPROXIMATING direct energy using CUBIC SPLINE INTERPOLATION
> | with 50.0 points per unit in tabled values
> | Relative Error Limit not exceeded for r .gt. 2.47
> | APPROXIMATING direct force using CUBIC SPLINE INTERPOLATION
> | with 50.0 points per unit in tabled values
> | Relative Error Limit not exceeded for r .gt. 2.90
>
>
> any idea?
>
>
> Thank in advance,
>
>
> Myriam
>
>
>
>
> ------------------------------
>
> Message: 9
> Date: Thu, 5 Mar 2020 17:35:29 +0000
> From: Gustaf Olsson <gustaf.olsson.lnu.se>
> Subject: Re: [AMBER] error job.sh
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <2d8dfb0d8e4f4a5eab58594a1d3b77ec.lnu.se>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Error Limit not exceeded
>
> Maybe I'm reading it wrong though it seems that this is reporting the absence of an error. Hence rather a status message than an error message.
>
> Does anything else happen?
>
> Best regards
> // Gustaf
> ________________________________
> Fr?n: MYRIAN TORRES RICO <myriam.torres.iiq.csic.es>
> Skickat: den 5 mars 2020 18:05:40
> Till: AMBER Mailing List
> ?mne: [AMBER] error job.sh
>
>
> Hi all,
>
> When I launch my script, this error appears:
>
> | APPROXIMATING direct energy using CUBIC SPLINE INTERPOLATION
> | with 50.0 points per unit in tabled values
> | Relative Error Limit not exceeded for r .gt. 2.47
> | APPROXIMATING direct force using CUBIC SPLINE INTERPOLATION
> | with 50.0 points per unit in tabled values
> | Relative Error Limit not exceeded for r .gt. 2.90
>
>
> any idea?
>
>
> Thank in advance,
>
>
> Myriam
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
> ------------------------------
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
> End of AMBER Digest, Vol 2932, Issue 1
> **************************************
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Received on Thu Mar 05 2020 - 18:30:01 PST
