Hi
Please try to follow amber tutorial first (1st tutorial from the link Sandra sent)
If you are still not able to reproduce the tutorial, let us know
Hai
> On Jul 18, 2016, at 11:17 AM, Vishal Nemaysh <vishal.bioinfotech.gmail.com> wrote:
>
> Respected sir,
>
> I have again tried to prepare my ligand and these are
> the commands which i have followed before using tleap
>
>
>
> *antechamber -i lig.pdb -fi pdb -o lig.mol2 -fo mol2antechamber -i lig.pdb
> -fi pdb -o lig.prepin -fo prepi -rn UNK -at amberparmchk -i lig.mol2 -f
> mol2 -o lig.frcmod*
>
> after that i have used the* tleap* and than used the following steps
>
> *tleap*
>
> *> source leaprc.gaff*
>
> *> source leaprc.ff10*
>
> *> source leaprc.ff12SB*
>
> *> list*
>
> *> b=loadpdb comp-lignew.pdb*
>
> *> check b*
>
> *> charge b*
>
> *> addions b Na+ 0.0*
>
> *> solvatebox b TIP3PBOX 10.0*
>
> *> saveamberparm b comp-lig_w_ions.prmtop comp-lig_w_ions.inpcrd*
>
>
> *and the final error is again like that*
>
>> saveamberparm b comp-lig_w_ions.prmtop comp-lig_w_ions.inpcrd
> Checking Unit.
> WARNING: There is a bond of 11.055190 angstroms between:
> ------- .R<NLEU 1>.A<CD1 12> and .R<UNK 364>.A<C14 12>
> WARNING: There is a bond of 13.966559 angstroms between:
> ------- .R<NLEU 1>.A<CG 10> and .R<UNK 364>.A<C16 11>
> WARNING: There is a bond of 13.213296 angstroms between:
> ------- .R<ARG 5>.A<C 23> and .R<UNK 364>.A<C23 1>
> WARNING: There is a bond of 15.592655 angstroms between:
> ------- .R<ARG 5>.A<CB 5> and .R<UNK 364>.A<C24 3>
>
> -- ignoring the warnings.
>
> Building topology.
> Building atom parameters.
> Building bond parameters.
> Could not find bond parameter for: 3C - C*
> Could not find bond parameter for: C - CZ
> Could not find bond parameter for: C8 - CZ
> Could not find bond parameter for: CM - F
> Could not find bond parameter for: CM - CZ
> Could not find bond parameter for: CZ - CM
> Could not find bond parameter for: CC - CZ
> Could not find bond parameter for: C* - CC
> Could not find bond parameter for: C* - CZ
> Could not find bond parameter for: C* - C
> Could not find bond parameter for: C* - C*
> Could not find bond parameter for: CZ - C*
> Could not find bond parameter for: CC - CZ
> Could not find bond parameter for: C* - CC
> Could not find bond parameter for: C* - C*
> Could not find bond parameter for: C* - CC
> Could not find bond parameter for: C - C*
> Could not find bond parameter for: CZ - N
> Could not find bond parameter for: NT - CZ
> Could not find bond parameter for: NT - CZ
> Could not find bond parameter for: CZ - NT
> Building angle parameters.
> Could not find angle parameter: CT - 3C - C*
> Could not find angle parameter: CT - 3C - C*
> Could not find angle parameter: CT - CC - C*
> Could not find angle parameter: HC - 3C - C*
> Could not find angle parameter: 3C - CT - CC
> Could not find angle parameter: 3C - C* - C*
> Could not find angle parameter: 3C - C* - CC
> Could not find angle parameter: 2C - 3C - C*
> Could not find angle parameter: O - C - CZ
> Could not find angle parameter: C - CZ - NT
> Could not find angle parameter: C8 - C8 - CZ
> Could not find angle parameter: HC - C8 - CZ
> Could not find angle parameter: HC - C8 - CZ
> Could not find angle parameter: C8 - CZ - NT
> Could not find angle parameter: CX - C8 - CZ
> Could not find angle parameter: CX - C - CZ
> Could not find angle parameter: N - C - CZ
> Could not find angle parameter: F - CM - CZ
> Could not find angle parameter: CZ - CM - F
> Could not find angle parameter: CZ - CM - CZ
> Could not find angle parameter: CZ - CZ - CM
> Could not find angle parameter: CC - C* - CZ
> Could not find angle parameter: CC - CZ - CZ
> Could not find angle parameter: C* - CC - CZ
> Could not find angle parameter: C* - CZ - CM
> Could not find angle parameter: NA - CC - C*
> Could not find angle parameter: NA - CC - CZ
> Could not find angle parameter: C - C* - C*
> Could not find angle parameter: C - NA - CC
> Could not find angle parameter: C* - C - NA
> Could not find angle parameter: C* - C - O
> Could not find angle parameter: C* - C* - CC
> Could not find angle parameter: C* - C* - CZ
> Could not find angle parameter: CZ - C* - C
> Could not find angle parameter: CZ - C* - C*
> Could not find angle parameter: CC - CZ - C*
> Could not find angle parameter: NA - CC - CZ
> Could not find angle parameter: CC - NA - CC
> Could not find angle parameter: C* - C* - CC
> Could not find angle parameter: C* - CC - NA
> Could not find angle parameter: C* - CC - CZ
> Could not find angle parameter: C* - C* - CC
> Could not find angle parameter: C* - CC - NA
> Could not find angle parameter: O - C - C*
> Could not find angle parameter: C - C* - C*
> Could not find angle parameter: C - C* - CC
> Could not find angle parameter: N - C - C*
> Could not find angle parameter: CZ - N - H
> Could not find angle parameter: CZ - N - C
> Could not find angle parameter: CZ - CZ - N
> Could not find angle parameter: CZ - NT - CZ
> Could not find angle parameter: NT - CZ - CZ
> Could not find angle parameter: CZ - NT - CZ
> Could not find angle parameter: CZ - NT - CZ
> Building proper torsion parameters.
> ** No torsion terms for HC-CT-3C-C*
> ** No torsion terms for HC-CT-3C-C*
> ** No torsion terms for HC-CT-3C-C*
> ** No torsion terms for CT-3C-CT-CC
> ** No torsion terms for CT-3C-C*-C*
> ** No torsion terms for CT-3C-C*-CC
> ** No torsion terms for HC-CT-3C-C*
> ** No torsion terms for HC-CT-3C-C*
> ** No torsion terms for HC-CT-3C-C*
> ** No torsion terms for CT-3C-C*-C*
> ** No torsion terms for CT-3C-C*-CC
> ** No torsion terms for CT-CC-C*-C
> ** No torsion terms for CT-CC-C*-C*
> ** No torsion terms for HC-3C-CT-CC
> ** No torsion terms for HC-3C-C*-C*
> ** No torsion terms for HC-3C-C*-CC
> ** No torsion terms for 3C-C*-C*-C
> ** No torsion terms for 3C-C*-C*-CC
> ** No torsion terms for 3C-C*-CC-NA
> ** No torsion terms for 3C-C*-CC-CZ
> ** No torsion terms for HC-2C-3C-C*
> ** No torsion terms for HC-2C-3C-C*
> ** No torsion terms for 2C-3C-CT-CC
> ** No torsion terms for 2C-3C-C*-C*
> ** No torsion terms for 2C-3C-C*-CC
> ** No torsion terms for CX-2C-3C-C*
> ** No torsion terms for O-C-CZ-NT
> ** No torsion terms for C-CZ-NT-CZ
> ** No torsion terms for C-CZ-NT-CZ
> ** No torsion terms for C8-C8-CZ-NT
> ** No torsion terms for HC-C8-CZ-NT
> ** No torsion terms for HC-C8-CZ-NT
> ** No torsion terms for C8-CZ-NT-CZ
> ** No torsion terms for C8-CZ-NT-CZ
> ** No torsion terms for CX-C8-CZ-NT
> ** No torsion terms for CX-C-CZ-NT
> ** No torsion terms for N-C-CZ-NT
> ** No torsion terms for CZ-CC-C*-CZ
> ** No torsion terms for CZ-CZ-CM-F
> ** No torsion terms for CZ-CZ-CM-CZ
> ** No torsion terms for CC-C*-CZ-CM
> ** No torsion terms for CC-CZ-CZ-CM
> ** No torsion terms for C*-CC-CZ-CZ
> ** No torsion terms for C*-CZ-CM-CZ
> ** No torsion terms for C*-CZ-CM-F
> ** No torsion terms for O-C-C*-C*
> ** No torsion terms for NA-C-C*-C*
> ** No torsion terms for NA-CC-C*-CZ
> ** No torsion terms for NA-CC-CZ-CZ
> ** No torsion terms for C-C*-C*-CC
> ** No torsion terms for C-C*-C*-CZ
> ** No torsion terms for C*-C*-CC-CZ
> ** No torsion terms for C*-C*-CC-NA
> ** No torsion terms for C*-C*-CZ-CM
> ** No torsion terms for CZ-C*-C-NA
> ** No torsion terms for CZ-C*-C-O
> ** No torsion terms for CZ-C*-C*-CC
> ** No torsion terms for CZ-C*-C*-CZ
> ** No torsion terms for CC-CZ-C*-C
> ** No torsion terms for CC-CZ-C*-C*
> ** No torsion terms for NA-CC-CZ-C*
> ** No torsion terms for CC-C*-C*-CC
> ** No torsion terms for C*-C*-CC-NA
> ** No torsion terms for C*-CC-CZ-C*
> ** No torsion terms for C*-3C-CT-CC
> ** No torsion terms for C*-C*-CC-NA
> ** No torsion terms for C*-C*-CC-CZ
> ** No torsion terms for O-C-C*-C*
> ** No torsion terms for O-C-C*-CC
> ** No torsion terms for C-C*-C*-CC
> ** No torsion terms for C-C*-CC-NA
> ** No torsion terms for N-C-C*-C*
> ** No torsion terms for N-C-C*-CC
> ** No torsion terms for CZ-CZ-N-H
> ** No torsion terms for CZ-CZ-N-C
> ** No torsion terms for CZ-NT-CZ-CZ
> ** No torsion terms for NT-CZ-CZ-N
> ** No torsion terms for CZ-NT-CZ-CZ
> Building improper torsion parameters.
> old PREP-specified impropers:
> <UNK 364>: C18 C20 N19 H39
> <UNK 364>: C15 N19 C18 O28
> <UNK 364>: C16 C18 C15 C14
> total 1140 improper torsions applied
> 3 improper torsions in old prep form
> Building H-Bond parameters.
> Incorporating Non-Bonded adjustments.
> Parameter file was not saved.
>
> *Sir I have attached my files which i used for it plz find it.*
>
> On Mon, Jul 18, 2016 at 6:51 PM, Aleksandra Skoric <
> skoricaleksandra.gmail.com> wrote:
>
>> Hi Vishal,
>>
>>
>> As could be seen from the leap message you don't have all parameters for
>> your ligand.
>>
>>
>>> Could not find bond parameter for
>>
>>
>> this means that you did not provide parameters, and you did not provide
>> them because you did not create them.
>>
>> If you open your lig.frcmod file you will see that the sections in your
>> frcmod file lack some parameters which is always denoted with ATTN, need
>> revision. Basically this means that your ligand in not fully described in
>> terms of atoms, bonds, angles etc.
>>
>>
>> You don’t have all the hydrogens on your ligand. You have to provide full
>> structure for non-standard residue in order to be able to make parameters.
>>
>>
>> Try to do amber tutorials http://ambermd.org/tutorials/#ligands
>>
>>
>> Best,
>>
>>
>> Sandra
>>
>>
>>
>> On Mon, Jul 18, 2016 at 1:58 PM, Bilal Nizami <nizamibilal1064.gmail.com>
>> wrote:
>>
>>> Hi Vishal,
>>>
>>> 2016-07-18 12:09 GMT+02:00 Vishal Nemaysh <vishal.bioinfotech.gmail.com
>>> :
>>>
>>>> Sir i have also attached the lig.mol2 and lig.frcmod file which i have
>>>> used.
>>>>
>>>> On Mon, Jul 18, 2016 at 3:01 PM, Vishal Nemaysh <
>>>> vishal.bioinfotech.gmail.com> wrote:
>>>>
>>>>> Respected Sir,
>>>>>
>>>>> plz help me regarding this problem i can't able to short out the same
>>> as
>>>> i
>>>>> have chacked as you suggested to me, but i can't find out the exect
>>>>> solution. please kindly help me.
>>>
>>>
>>> As Hai suggested, look into the amber mailing list. Such error have been
>>> addressed already.
>>>
>>> or
>>>
>>> Can you please give more details of steps you have done. It seems you
>> have
>>> some missing parameters in your .frcmod file (lines with ATTN, need
>>> revision).
>>>
>>> Regards,
>>>
>>>
>>>
>>>>
>>>>> On Sun, Jul 17, 2016 at 11:45 PM, Hai Nguyen <nhai.qn.gmail.com>
>>> wrote:
>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> this is a typical error. Can you try to follow those first
>>>>>>
>>>>>> http://archive.ambermd.org/201004/0574.html
>>>>>>
>>>>>> other topics
>> https://www.google.com/search?q=WARNING%3A+There+is+a+bond+of+11.055252+angstroms+between%3A&rlz=1C1CHMO_enUS485US485&oq=WARNING%3A+There+is+a+bond+of+11.055252+angstroms+between%3A&aqs=chrome..69i57j69i58&sourceid=chrome&ie=UTF-8#q=WARNING:+There+is+a+bond+of+angstroms+between
>>>>>> :
>>>>>>
>>>>>> Hai
>>>>>>
>>>>>> On Sun, Jul 17, 2016 at 1:52 PM, Vishal Nemaysh <
>>>>>> vishal.bioinfotech.gmail.com> wrote:
>>>>>>
>>>>>>> Respected Sir,
>>>>>>> I have faced the problem when i saved the
>>>> .prmtop
>>>>>>> and .inpcrd fileby appling the following command: but it will
>> showed
>>>> the
>>>>>>> following error. how can i resolve it. the pdb complex file is
>>>> attached
>>>>>>> herewith plz check the same.
>>>>>>>
>>>>>>> *> saveamberparm b comp-lig_w_ions.prmtop comp-lig_w_ions.inpcrd*
>>>>>>> Checking Unit.
>>>>>>> WARNING: There is a bond of 11.055252 angstroms between:
>>>>>>> ------- .R<NLEU 1>.A<CD1 12> and .R<UNK 364>.A<C14 12>
>>>>>>> WARNING: There is a bond of 13.966544 angstroms between:
>>>>>>> ------- .R<NLEU 1>.A<CG 10> and .R<UNK 364>.A<C16 11>
>>>>>>> WARNING: There is a bond of 13.213808 angstroms between:
>>>>>>> ------- .R<ARG 5>.A<C 23> and .R<UNK 364>.A<C23 1>
>>>>>>> WARNING: There is a bond of 15.593765 angstroms between:
>>>>>>> ------- .R<ARG 5>.A<CB 5> and .R<UNK 364>.A<C24 3>
>>>>>>>
>>>>>>> -- ignoring the warnings.
>>>>>>>
>>>>>>> Building topology.
>>>>>>> Building atom parameters.
>>>>>>> Building bond parameters.
>>>>>>> Could not find bond parameter for: 3C - C*
>>>>>>> Could not find bond parameter for: C - CZ
>>>>>>> Could not find bond parameter for: C8 - CZ
>>>>>>> Building angle parameters.
>>>>>>> Could not find angle parameter: CT - 3C - C*
>>>>>>> Could not find angle parameter: CT - 3C - C*
>>>>>>> Could not find angle parameter: CT - CC - C*
>>>>>>> Could not find angle parameter: HC - 3C - C*
>>>>>>> Could not find angle parameter: 3C - CT - CC
>>>>>>> Could not find angle parameter: 3C - C* - C*
>>>>>>> Could not find angle parameter: 3C - C* - CC
>>>>>>> Could not find angle parameter: 2C - 3C - C*
>>>>>>> Could not find angle parameter: O - C - CZ
>>>>>>> Could not find angle parameter: C - CZ - NT
>>>>>>> Could not find angle parameter: C8 - C8 - CZ
>>>>>>> Could not find angle parameter: HC - C8 - CZ
>>>>>>> Could not find angle parameter: HC - C8 - CZ
>>>>>>> Could not find angle parameter: C8 - CZ - NT
>>>>>>> Could not find angle parameter: CX - C8 - CZ
>>>>>>> Could not find angle parameter: CX - C - CZ
>>>>>>> Could not find angle parameter: N - C - CZ
>>>>>>> Building proper torsion parameters.
>>>>>>> ** No torsion terms for HC-CT-3C-C*
>>>>>>> ** No torsion terms for HC-CT-3C-C*
>>>>>>> ** No torsion terms for HC-CT-3C-C*
>>>>>>> ** No torsion terms for CT-3C-CT-CC
>>>>>>> ** No torsion terms for CT-3C-C*-C*
>>>>>>> ** No torsion terms for CT-3C-C*-CC
>>>>>>> ** No torsion terms for HC-CT-3C-C*
>>>>>>> ** No torsion terms for HC-CT-3C-C*
>>>>>>> ** No torsion terms for HC-CT-3C-C*
>>>>>>> ** No torsion terms for CT-3C-C*-C*
>>>>>>> ** No torsion terms for CT-3C-C*-CC
>>>>>>> ** No torsion terms for CT-CC-C*-C
>>>>>>> ** No torsion terms for CT-CC-C*-C*
>>>>>>> ** No torsion terms for HC-3C-CT-CC
>>>>>>> ** No torsion terms for HC-3C-C*-C*
>>>>>>> ** No torsion terms for HC-3C-C*-CC
>>>>>>> ** No torsion terms for 3C-C*-C*-C
>>>>>>> ** No torsion terms for 3C-C*-C*-CC
>>>>>>> ** No torsion terms for 3C-C*-CC-NA
>>>>>>> ** No torsion terms for 3C-C*-CC-CZ
>>>>>>> ** No torsion terms for HC-2C-3C-C*
>>>>>>> ** No torsion terms for HC-2C-3C-C*
>>>>>>> ** No torsion terms for 2C-3C-CT-CC
>>>>>>> ** No torsion terms for 2C-3C-C*-C*
>>>>>>> ** No torsion terms for 2C-3C-C*-CC
>>>>>>> ** No torsion terms for CX-2C-3C-C*
>>>>>>> ** No torsion terms for O-C-CZ-NT
>>>>>>> ** No torsion terms for C-CZ-NT-CZ
>>>>>>> ** No torsion terms for C-CZ-NT-CZ
>>>>>>> ** No torsion terms for C8-C8-CZ-NT
>>>>>>> ** No torsion terms for HC-C8-CZ-NT
>>>>>>> ** No torsion terms for HC-C8-CZ-NT
>>>>>>> ** No torsion terms for C8-CZ-NT-CZ
>>>>>>> ** No torsion terms for C8-CZ-NT-CZ
>>>>>>> ** No torsion terms for CX-C8-CZ-NT
>>>>>>> ** No torsion terms for CX-C-CZ-NT
>>>>>>> ** No torsion terms for N-C-CZ-NT
>>>>>>> ** No torsion terms for C*-3C-CT-CC
>>>>>>> Building improper torsion parameters.
>>>>>>> old PREP-specified impropers:
>>>>>>> <UNK 364>: C18 C20 N19 H39
>>>>>>> <UNK 364>: C15 N19 C18 O28
>>>>>>> <UNK 364>: C16 C18 C15 C14
>>>>>>> total 1146 improper torsions applied
>>>>>>> 3 improper torsions in old prep form
>>>>>>> Building H-Bond parameters.
>>>>>>> Incorporating Non-Bonded adjustments.
>>>>>>> Parameter file was not saved.
>>>>>>>
>>>>>>> thankyou in advance....
>>>>>>>
>>>>>>> --
>>>>>>> Vishal Nemaysh
>>>>>>> Research Scholar,
>>>>>>> Neuropharmaceutical Chemistry Group,
>>>>>>> Dr. B. R. Ambedkar Center for Biomedical Research,
>>>>>>> University of Delhi, Delhi-110007
>>>>>>> Email: *vishal.bioinfotech.gmail.com <
>> vishal.bioinfotech.gmail.com
>>>> *
>>>>>>> Phone: 91-11-27662778 Mobile: 91+8447581401, 91+9650736653
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> 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
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Vishal Nemaysh
>>>>> Research Scholar,
>>>>> Neuropharmaceutical Chemistry Group,
>>>>> Dr. B. R. Ambedkar Center for Biomedical Research,
>>>>> University of Delhi, Delhi-110007
>>>>> Email: *vishal.bioinfotech.gmail.com <vishal.bioinfotech.gmail.com>*
>>>>> Phone: 91-11-27662778 Mobile: 91+8447581401, 91+9650736653
>>>>
>>>>
>>>>
>>>> --
>>>> Vishal Nemaysh
>>>> Research Scholar,
>>>> Neuropharmaceutical Chemistry Group,
>>>> Dr. B. R. Ambedkar Center for Biomedical Research,
>>>> University of Delhi, Delhi-110007
>>>> Email: *vishal.bioinfotech.gmail.com <vishal.bioinfotech.gmail.com>*
>>>> Phone: 91-11-27662778 Mobile: 91+8447581401, 91+9650736653
>>>>
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>>
>>> --
>>> *Bilal Nizami*
>>> School of Health Sciences
>>> University of KwaZulu-Natal
>>> Durban
>>> 4000
>>> South Africa
>>>
>>> Linkedin: za.linkedin.com/pub/bilal-nizami/49/673/790/
>>> Email: 214573074.stu.ukzn.ac.za
>>> _______________________________________________
>>> 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
>
>
>
> --
> Vishal Nemaysh
> Research Scholar,
> Neuropharmaceutical Chemistry Group,
> Dr. B. R. Ambedkar Center for Biomedical Research,
> University of Delhi, Delhi-110007
> Email: *vishal.bioinfotech.gmail.com <vishal.bioinfotech.gmail.com>*
> Phone: 91-11-27662778 Mobile: 91+8447581401, 91+9650736653
> <comp-lignew.pdb>
> <lig.frcmod>
> <lig.mol2>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Mon Jul 18 2016 - 09:30:03 PDT
