Hi everyone
I ran the go9 for geometry optimization command g09 < ox_small_opt.com >
ox_small_opt.log after that this error come
here 88 position is Fe. Kindly guide How i can remove this error. I
prepared the input files with the help of MCPB.py.
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
Berny optimization.
Using GEDIIS/GDIIS optimizer.
Bend failed for angle 20 - 88 - 57
Tors failed for dihedral 37 - 20 - 88 - 57
Tors failed for dihedral 53 - 20 - 88 - 57
Tors failed for dihedral 39 - 57 - 88 - 20
Tors failed for dihedral 55 - 57 - 88 - 20
FormBX had a problem.
Error termination via Lnk1e in /nfs/amino-projects/rrkhalid/g09/l103.exe
at Mon Jul 17 06:00:12 2017.
Job cpu time: 2 days 1 hours 48 minutes 59.2 seconds.
File lengths (MBytes): RWF= 596 Int= 0 D2E= 0 Chk= 52
Scr= 1
On Fri, Jun 30, 2017 at 12:31 AM, Andrew Schaub <aschaub.uci.edu> wrote:
> If you have an account on the HPC to run Amber, then your account probably
> already has access to Gaussian. The people at ARC-TS should be able to help
> you with the Gaussian portion of this, then you'll take the output from
> Gaussian and feed it back into MCPB. Your almost there.
>
> Good Luck!
>
> Drew
>
> On Thu, Jun 29, 2017 at 9:26 PM, Rana Rehan Khalid <rrkhalid.umich.edu>
> wrote:
>
> > So in that case is there any other way use mcpb.py input files like go3
> >
> > On Jun 30, 2017 12:19 AM, "Elvis Martis" <elvis.martis.bcp.edu.in>
> wrote:
> >
> > > Hi Rana,
> > >
> > > "g03" is a Gaussian 03 command and Gaussian 03 or 09 or 2016 is not a
> > part
> > > of AMBER or AMBERTOOLS and has to be purchased separately.
> > >
> > >
> > > Best Regards
> > >
> > > [photo]
> > >
> > >
> > >
> > > Elvis Martis
> > > Ph.D. Student (Computational Chemistry)
> > > at Bombay College of Pharmacy
> > >
> > >
> > > A Kalina, Santacruz [E], Mumbai 400098, INDIA
> > > W www.elvismartis.in<https://webapp.wisestamp.com/www.elvismartis.in>
> > > Skype. adrian_elvis12<https://webapp.wisestamp.com/#>
> > >
> > >
> > > [https://ci3.googleusercontent.com/proxy/P0F8-p0kwxKdscp6zsT-
> > > ZSRttk9OJEsBGiaXej_H2ERz8n2ma5SLHFAWJdKL-wqOlXSGjbmEyga9C8lmU1bs-_
> > > yPIq3CnazA5eJVDYjce1r-34uwxqjjRnmAtE473lEq28nSHQ=s0-
> > > d-e1-ft#https://s3.amazonaws.com/images.wisestamp.com/
> > > icons_for_colors_32/linkedin.png]<http://www.linkedin.com/
> > > in/elvisadrianmartis/>
> > >
> > >
> > >
> > >
> > >
> > > ________________________________
> > > From: Rana Rehan Khalid <rrkhalid.umich.edu>
> > > Sent: 30 June 2017 09:45:47
> > > To: AMBER Mailing List
> > > Subject: Re: [AMBER] MCPB.py error (MCPB.py -i 4ZF6.in -s 1) use
> default
> > > ions 7440
> > >
> > > this command is not working Andrew i am using amber 16 is go3 not
> > buitin
> > > i have all the input files for this command
> > >
> > > g03 < 4ZF6_small_opt.com
> > > <http://ambermd.org/tutorials/advanced/tutorial20/files/
> > > mcpbpy_heme/4ZF6_small_opt.com>
> > > > 4ZF6_small_opt.log
> > >
> > > On Thu, Jun 29, 2017 at 11:30 PM, Rana Rehan Khalid <
> rrkhalid.umich.edu>
> > > wrote:
> > >
> > > > oh yes it run now. Andrew i use
> > > >
> > > > 2.000000 charge for FE ferrous oxidation state
> > > >
> > > > and use 2.8 cutoff by default from the 4ZF6 <
> > > http://ambermd.org/tutorials/advanced/tutorial20/files/
> > mcpbpy_heme/4ZF6.in>.in
> > > file. is it write ??
> > > >
> > > >
> > > > On Thu, Jun 29, 2017 at 11:18 PM, Andrew Schaub <aschaub.uci.edu>
> > wrote:
> > > >
> > > >> Based off of your output, and lack of an .input file, I am assuming
> > the
> > > >> following. You most likely copied the input script from the
> tutorial,
> > > but
> > > >> forgot to change the ions_id.
> > > >>
> > > >> original_pdb 4ZF6_H_renum.pdb
> > > >> group_name 4ZF6
> > > >> cut_off 2.8
> > > >> *ion_ids 7440*
> > > >> software_version g09
> > > >> ion_mol2files FE.mol2
> > > >> naa_mol2files HEM.mol2 1PE.mol2 EDO.mol2
> > > >> frcmod_files HEM.frcmod 1PE.frcmod EDO.frcmod
> > > >>
> > > >> If you open up your HNOXO_H_renum.pdb, scroll down to where the Fe
> is,
> > > and
> > > >> find the atom number. Change your ions_id to match the atom number
> > > there.
> > > >> In the original tutorial, the Fe atom ID was pulled from
> > > 4ZF6_H_renum.pdb,
> > > >> by finding this line in the PDB file:
> > > >>
> > > >> HETATM *7440 FE* FE A 462 -7.890 0.888 28.105 1.00
> > > >> 38.80 FE
> > > >>
> > > >> Best Regards,
> > > >>
> > > >> Drew
> > > >>
> > > >>
> > > >>
> > > >>
> > > >> On Thu, Jun 29, 2017 at 7:44 PM, Rana Rehan Khalid <
> > rrkhalid.umich.edu>
> > > >> wrote:
> > > >> >
> > > >> > The following is the input variable you have:
> > > >> > The variable ion_ids is : [7440]
> > > >> > The variable ion_info is : []
> > > >> > The variable ion_mol2files is : ['FE.mol2']
> > > >> > The variable original_pdb is : HNOXO_H_renum.pdb
> > > >> > The variable add_bonded_pairs is : []
> > > >> > The variable additional_resids is : []
> > > >> > The variable anglefc_avg is : 0
> > > >> > The variable bondfc_avg is : 0
> > > >> > The variable cut_off is : 2.8
> > > >> > The variable chgfix_resids is : []
> > > >> > The variable force_field is : ff14SB
> > > >> > The variable frcmodfs is : ['HEM.frcmod']
> > > >> > The variable gaff is : 1
> > > >> > The variable group_name is : HNOXO
> > > >> > The variable ion_paraset is : CM (Only for nonbonded model)
> > > >> > The variable large_opt is : 0
> > > >> > The variable lgmodel_chg is : -99
> > > >> > -99 means program will assign a charge automatically.
> > > >> > The variable naa_mol2files is : ['HEM.mol2']
> > > >> > The variable scale_factor is : 1.0
> > > >> > ATTENTION: This is the scale factor of frequency. The
> > > >> > force constants will be scaled by multiplying the
> > square
> > > >> > of scale_factor.
> > > >> > The variable smmodel_chg is : -99
> > > >> > -99 means program will assign a charge automatically.
> > > >> > The variable software_version is : g09
> > > >> > The variable sqm_opt is : 0
> > > >> > The variable water_model is : TIP3P
> > > >> > Traceback (most recent call last):
> > > >> > File "/home/rehan/Downloads/amber16/bin/MCPB.py", line 498, in
> > > >> <module>
> > > >> > addbpairs)
> > > >> > File
> > > >> >
> > > >> "/home/rehan/Downloads/amber16/lib/python2.7/site-packages/
> > > >> mcpb/gene_model_files.py",
> > > >> > line 50, in get_ms_resnames
> > > >> > resid = mol.atoms[i].resid
> > > >> > KeyError: 7440
> > > >> > _______________________________________________
> > > >> > AMBER mailing list
> > > >> > AMBER.ambermd.org
> > > >> > http://lists.ambermd.org/mailman/listinfo/amber
> > > >>
> > > >>
> > > >>
> > > >>
> > > >> --
> > > >> Andrew Schaub
> > > >> Graduate Program in Chemical & Structural Biology
> > > >> Tsai Lab, http:///www.tsailabuci.com/
> > > >> Luo Lab, http://rayl0.bio.uci.edu/html/
> > > >> University of California, Irvine
> > > >> Irvine, CA 92697-2280
> > > >> 949-824-8829 (lab)
> > > >> 949-877-9380 (cell)
> > > >> aschaub.uci.edu
> > > >> _______________________________________________
> > > >> 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
> > > _______________________________________________
> > > 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
> >
>
>
>
> --
> Andrew Schaub
> Graduate Program in Chemical & Structural Biology
> Tsai Lab, http:///www.tsailabuci.com/ <http://www.tsailabuci.com/>
> Luo Lab, http://rayl0.bio.uci.edu/html/
> University of California, Irvine
> Irvine, CA 92697-2280
> 949-824-8829 (lab)
> 949-877-9380 (cell)
> aschaub.uci.edu <http://www.linkedin.com/pub/andrew-schaub/9a/907/382/>
> _______________________________________________
> 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
Received on Mon Jul 17 2017 - 13:00:03 PDT
