If any of your residues GLU or ASP are supposed to be protonated, you need to change the rename from ASP to ASH and GLU to GLH, etc in your pub file before loading it to tleap. This could be why you are getting this error.
> On Jul 9, 2019, at 9:04 AM, shivangi agarwal <shiviagarwalpharma.gmail.com> wrote:
>
> Thanks, loaded source.leaprc.protein.ff14SB, recognized residues but showe
> error as
>> com=loadpdb complex.pdb
> Loading PDB file: ./complex_42_noH_no_HOH_2.pdb
> (starting new molecule for chain )
> -- residue 512: duplicate [ C] atoms (total 21)
> -- residue 512: duplicate [ N] atoms (total 5)
> -- residue 512: duplicate [ O] atoms (total 4)
>
> Warning: Atom names in each residue should be unique.
> (Same-name atoms are handled by using the first
> occurrence and by ignoring the rest.
> Frequently duplicate atom names stem from alternate
> conformations in the PDB file.)
>
> Added missing heavy atom: .R<GLU 165>.A<CG 8>
> Added missing heavy atom: .R<GLU 165>.A<CD 11>
> Added missing heavy atom: .R<GLU 165>.A<OE1 12>
> Added missing heavy atom: .R<GLU 165>.A<OE2 13>
> Added missing heavy atom: .R<ASP 236>.A<CG 8>
> Added missing heavy atom: .R<ASP 236>.A<OD1 9>
> Added missing heavy atom: .R<ASP 236>.A<OD2 10>
> Created a new atom named: OXT within residue: .R<PRO 259>
> Added missing heavy atom: .R<GLU 416>.A<CG 8>
> Added missing heavy atom: .R<GLU 416>.A<CD 11>
> Added missing heavy atom: .R<GLU 416>.A<OE1 12>
> Added missing heavy atom: .R<GLU 416>.A<OE2 13>
> Added missing heavy atom: .R<ASP 487>.A<CG 8>
> Added missing heavy atom: .R<ASP 487>.A<OD1 9>
> Added missing heavy atom: .R<ASP 487>.A<OD2 10>
> Added missing heavy atom: .R<LIG 512>.A<N4 26>
> Added missing heavy atom: .R<LIG 512>.A<C18 23>
> Added missing heavy atom: .R<LIG 512>.A<O1 28>
> Added missing heavy atom: .R<LIG 512>.A<C17 22>
> Added missing heavy atom: .R<LIG 512>.A<C19 24>
> Added missing heavy atom: .R<LIG 512>.A<C16 21>
> Added missing heavy atom: .R<LIG 512>.A<C20 25>
> Added missing heavy atom: .R<LIG 512>.A<C15 20>
> Added missing heavy atom: .R<LIG 512>.A<N3 19>
> Added missing heavy atom: .R<LIG 512>.A<C14 18>
> Added missing heavy atom: .R<LIG 512>.A<N2 17>
> Added missing heavy atom: .R<LIG 512>.A<O2 29>
> Added missing heavy atom: .R<LIG 512>.A<C6 7>
> Added missing heavy atom: .R<LIG 512>.A<C7 9>
> Added missing heavy atom: .R<LIG 512>.A<C4 5>
> Added missing heavy atom: .R<LIG 512>.A<O3 30>
> Added missing heavy atom: .R<LIG 512>.A<N1 10>
> Added missing heavy atom: .R<LIG 512>.A<C8 11>
> Added missing heavy atom: .R<LIG 512>.A<C3 4>
> Added missing heavy atom: .R<LIG 512>.A<C5 6>
> Added missing heavy atom: .R<LIG 512>.A<C9 12>
> Added missing heavy atom: .R<LIG 512>.A<C13 16>
> Added missing heavy atom: .R<LIG 512>.A<C2 3>
> Added missing heavy atom: .R<LIG 512>.A<C10 13>
> Added missing heavy atom: .R<LIG 512>.A<C12 15>
> Added missing heavy atom: .R<LIG 512>.A<C1 2>
> Added missing heavy atom: .R<LIG 512>.A<C11 14>
> total atoms in file: 3913
> Leap added 3862 missing atoms according to residue templates:
> 41 Heavy
> 3821 H / lone pairs
> The file contained 1 atoms not in residue templates
>> saveAmberParm com see.inpcrd see.prmtop
> Checking Unit.
>
> Warning: There is a bond of 40.101967 angstroms between:
>
> Warning: There is a bond of 14.630144 angstroms between:
>
> Warning: There is a bond of 8.520137 angstroms between:
>
> Warning: There is a bond of 6.768709 angstroms between:
>
> Warning: The unperturbed charge of the unit (-14.001000) is not zero.
> *FATAL: Atom .R<PRO 259>.A<OXT 15> does not have a type.*
>
> Error: Failed to generate parameters
>
> Warning: Parameter file was not saved.
>
> On Tue, Jul 9, 2019 at 6:28 PM Santanu Santra <santop420.gmail.com> wrote:
>
>> Dear Shivangi,
>>
>> I guess you forgot to load corresponding leaprc file for protein . Because
>> once you have loaded leaprc file for protein it will recognize all the
>> amino acid rresidues. Hope this will work. Thanks and Regards.
>> Santanu Santra
>>
>> On Tue, Jul 9, 2019 at 6:23 PM shivangi agarwal <
>> shiviagarwalpharma.gmail.com> wrote:
>>
>>> Thanks for your reply.
>>>
>>> I have installed AmberTools19. When I am loading my protein
>> _ligand_complex
>>> file (complex loadpdb complex.pdb), it is showing error.
>>> I am hereby attaching error message and complex.pdb
>>> Kindly suggest.
>>>
>>> On Tue, Jul 9, 2019 at 10:26 AM somdev pahari <somdevpahari1.gmail.com>
>>> wrote:
>>>
>>>> Dear Shivangi,
>>>>
>>>> Yes, you can install AmberTools 19 with Amber12. Here I paste a
>> link.
>>>>
>> http://jswails.wikidot.com/installing-ambertools-14-and-older-amber
>>>> Hope it will help you.
>>>>
>>>> Regards
>>>> Somdev Pahari
>>>> PhD Scholar
>>>> NIT Rourkela
>>>> India
>>>>
>>>> On Tue, Jul 9, 2019 at 9:40 AM shivangi agarwal <
>>>> shiviagarwalpharma.gmail.com> wrote:
>>>>
>>>>> I have downloaded AmberTools 19. Will the same license key work for
>>>>> AmberTools 19 as for Amber12?.
>>>>>
>>>>>
>>>>>
>>>>> Regards
>>>>> Shivangi
>>>>>
>>>>> On Mon, Jul 8, 2019 at 6:58 PM Daniel Roe <daniel.r.roe.gmail.com>
>>>> wrote:
>>>>>
>>>>>> On Mon, Jul 8, 2019 at 3:41 AM shivangi agarwal
>>>>>> <shiviagarwalpharma.gmail.com> wrote:
>>>>>>>
>>>>>>> Hereby, i am attaching my terminal commands which I have given.
>>>>>>> Please go through the commands and suggest me a possible solution
>>> to
>>>>> come
>>>>>>> out of this error.
>>>>>>
>>>>>> Did you follow the advice previously given to you and try
>> AmberTools
>>>>>> 19, read chapter 3, etc? Your output still shows you as using Amber
>>>>>> 12, which is extremely out of date. It also shows a warning at the
>>>>>> very beginning (about assigned bond types being wrong). Have you
>>>>>> attempted to look into this? How did you generate ligand2.pdb?
>>>>>>
>>>>>> The tutorial you are following is categorized as advanced. I highly
>>>>>> recommend that you try to complete some of the basic tutorials
>> first
>>>>>> so you can get a better feel for what antechamber/leap are trying
>> to
>>>>>> do, which in turn will give you the tools to better troubleshoot
>>> these
>>>>>> issues.
>>>>>>
>>>>>> -Dan
>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Thanks and regards
>>>>>>> Shivangi Agarwal
>>>>>>>
>>>>>>> On Wed, Jul 3, 2019 at 11:15 PM David Case <
>> david.case.rutgers.edu
>>>>
>>>>>> wrote:
>>>>>>>
>>>>>>>> On Wed, Jul 03, 2019, shivangi agarwal wrote:
>>>>>>>>
>>>>>>>>> For atom: .R<ZN 260>.A<ZN 1> Could not find type: Zn2+
>>>>>>>>>
>>>>>>>>> *antechamber -i ligand.pdb -fi pdb -o ligand.mol2 -fo mol2 -c
>>> bcc
>>>> -s
>>>>>>>>> 2parmchk -i ligand.mol2 -f mol2 -o ligand.frcmodtleapsource
>>>>>>>>> leaprc.ff99SBsource leaprc.gaffLIG=loadmol2
>> ligand.mol2listcheck
>>>>>>>>> LIGloadamberparams ligand.frcmodsaveoff LIG
>>>> ligand.libsaveamberparm
>>>>>> LIG
>>>>>>>>> ligand.prmtop ligand.inpcrdquittleap -s -f Zn.intleapsource
>>>>>>>>> leaprc.ff99SBsource leaprc.gaffloadamberparams
>>>> ligand.frcmodloadoff
>>>>>>>>> atomic_ions.libloadoff ligand.libcomplex =loadpdb
>>>>>> rec_lig.pdbsaveamberparm
>>>>>>>>> complex rec_lig.prmtop rec_lig.inpcrdsavepdb complex
>>> rec_lig.pdb*
>>>>>>>>
>>>>>>>> Your email program (or maybe mine?) has made it very hard to
>> read
>>>> the
>>>>>>>> above. But it looks like you are using a very old version of
>>>>>>>> AmberTools, since we have not had a "leaprc.ff99SB" in the
>> search
>>>>> path
>>>>>>>> for many years. I suspect that you are never loading the
>>>> parameters
>>>>>> for
>>>>>>>> ions like zinc.
>>>>>>>>
>>>>>>>> I think you are going to have to download AmberTools19, and
>> read
>>>>>> Chapter
>>>>>>>> 3 about how force fields are loaded. You can keep your old
>>>> ligand.*
>>>>>>>> files. The default approach will treat interactions between
>> zinc
>>>> and
>>>>>>>> other atoms as non-bonded ones. You'll have to see if this
>> meets
>>>>> your
>>>>>>>> needs. If not, consult sections 15.7 and 15.8 in the manual,
>>> which
>>>>>>>> discusses ways to handle metals.
>>>>>>>>
>>>>>>>> ...good luck....dac
>>>>>>>>
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> 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
>>>>>
>>>> _______________________________________________
>>>> 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
>>>
>>
>>
>> --
>> Santanu Santra
>> Research Scholar
>> Molecular Simulation Laboratory
>> Department of Chemistry
>> NIT ROURKELA
>> ROURKELA, 769008
>> _______________________________________________
>> 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
Received on Tue Jul 09 2019 - 06:30:03 PDT
