Hi Rana,
I think you met similar problem as a former email which you sent to me independently. The solution is similar. Please let me know your trying and difficulties you met to solve the problem.
Kind regards,
Pengfei
> On Jul 1, 2017, at 8:40 PM, Rana Rehan Khalid <rrkhalid.umich.edu> wrote:
>
> after running this command i found this error """MCPB.py -i NO.in -s
> 1"""
> Totally there are 313 electrons in the large model.
> Traceback (most recent call last):
> File "/home/rehan/Downloads/amber16/bin/MCPB.py", line 562, in <module>
> premol2fs, cutoff, watermodel, 2, largeopt, sqmopt, smchg, lgchg)
> File
> "/home/rehan/Downloads/amber16/lib/python2.7/site-packages/mcpb/gene_model_files.py",
> line 1745, in gene_model_files
> ionids, chargedict, lgchg, outf, watermodel, largeopt, sqmopt)
> File
> "/home/rehan/Downloads/amber16/lib/python2.7/site-packages/mcpb/gene_model_files.py",
> line 1441, in build_large_model
> chargedict, IonLJParaDict, largeopt)
> File
> "/home/rehan/Downloads/amber16/lib/python2.7/site-packages/msmtmol/gauio.py",
> line 156, in write_gau_mkf
> chg = int(round(chargedict[ionname], 0))
> KeyError: 'O02'
>
> On Sat, Jul 1, 2017 at 8:57 PM, Andrew Schaub <aschaub.uci.edu> wrote:
>
>> You need to add the '-m' flag to specify your multiplicity. Remember,
>> nitric oxide has one free electron as it's a radical, so it's at least a
>> doublet (and not a singlet). So adding '-m 2' would probably fix your
>> problem. If you are just going to transfer the mol2 to the MCPB.py script
>> then it's not neccessary to add charges.
>>
>> antechamber -fi pdb -fo mol2 -i NIT.pdb -o NIT.mol2 -pf y
>>
>> On Sat, Jul 1, 2017 at 5:47 PM, Rana Rehan Khalid <rrkhalid.umich.edu>
>> wrote:
>>
>>> I tried to produce the mol2 file for Nitric oxide (NO) following error
>> come
>>> kindly guide me
>>> antechamber -fi pdb -fo mol2 -i NIT_H_renum.pdb -o NIT.mol2 -c bcc -pf y
>>> -nc 0
>>>
>>> Info: Bond types are assigned for valence state 2 with penalty of 3
>>> Total number of electrons: 15; net charge: 0
>>> INFO: Number of electrons is odd: 15
>>> Please check the total charge (-nc flag) and spin multiplicity (-m
>>> flag)
>>>
>>> Running: /home/rehan/Downloads/amber16/bin/sqm -O -i sqm.in -o sqm.out
>>> Error: cannot run "/home/rehan/Downloads/amber16/bin/sqm -O -i sqm.in -o
>>> sqm.out" of bcc() in charge.c properly, exit
>>>
>>> On Fri, Jun 30, 2017 at 2:35 AM, Andrew Schaub <aschaub.uci.edu> wrote:
>>>
>>>> Are you trying to run two different simulations? One with nitric oxide
>>> (NO)
>>>> bound? One with dioxygen (O-O) bound? If so, you can just change an
>>> oxygen
>>>> in your dioxygen bound complex to a nitrogen, save that and run MCPB
>> ont
>>>> hat system as well. You would run both simulations, and then compare
>> the
>>>> results of the two to look for differences. I believe the Poulos lab
>> has
>>>> done some MD studies on NO in P450s:
>>>> https://www.ncbi.nlm.nih.gov/pubmed/26448477
>>>> https://www.ncbi.nlm.nih.gov/pubmed/27439869
>>>>
>>>> Fortunately heme-bound enzymes are very well studied (for example
>>> myoglobin
>>>> and hemoglobin), so there is a wealth of information on electronic
>>>> structure calculations and molecular dynamics simulations. Those two
>>> review
>>>> papers I mentioned from ACS Chem Rev is a good place to start. I would
>>>> recommend searching the primary literature to see what protocols and
>>>> methods others have used to study heme bound systems to get an idea of
>>> what
>>>> type of analysis or system setups you will need to perform. I just
>> wanted
>>>> to warn you, I've had limited experience with heme simulations, and
>> have
>>>> found them to be very inflexible, and almost rock-like compared to
>> other
>>>> enzymes I have studied in silico. I had to use accelerated sampling
>>>> techniques to get useful data.
>>>>
>>>> Good Luck!
>>>>
>>>> Drew
>>>>
>>>> On Thu, Jun 29, 2017 at 10:03 PM, Rana Rehan Khalid <
>> rrkhalid.umich.edu>
>>>> wrote:
>>>>
>>>>> Andrew one more thing i want to ask , i prepare the file for heme
>>>>> containing protein but in our case the heme fe-----NO in one system
>> and
>>>>> other it bonded with O2 how i can add it because i need to study when
>>> NO
>>>>> attach AND when O2 attach what changes occur so in that case how i
>> add
>>> NO
>>>>> and O2 in the system
>>>>>
>>>>> On Fri, Jun 30, 2017 at 12:38 AM, Rana Rehan Khalid <
>>> rrkhalid.umich.edu>
>>>>> wrote:
>>>>>
>>>>>> That's great
>>>>>>
>>>>>> On Jun 30, 2017 12:30 AM, "Andrew Schaub" <aschaub.uci.edu> wrote:
>>>>>>
>>>>>>> As Elvis stated. You need Gaussian. But good news, The University
>> of
>>>>>>> Michigan has access to it. http://arc-ts.umich.edu/
>>> software/gaussian/
>>>>>>>
>>>>>>> Best Regards,
>>>>>>>
>>>>>>> Drew
>>>>>>>
>>>>>>>
>>>>>>> On Thu, Jun 29, 2017 at 9:15 PM, Rana Rehan Khalid <
>>>> rrkhalid.umich.edu>
>>>>>>> wrote:
>>>>>>>
>>>>>>>> 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/mcpbp
>>>>>>> y_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
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> 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
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> 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
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>>>>
>>> _______________________________________________
>>> AMBER mailing list
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>>> 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
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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Received on Mon Jul 03 2017 - 10:30:02 PDT
