Hi,
It seems that You wish to use shortcut instead to carefully read, repeat and
finally apply (your case) Amber tutorial (manual as well) pages. That’s all
what you need. I do not think You have bonded ligand (sunitinib isn't it?).
Just follow advice from Sandra and good luck.
Cheers
Zoran
-----Original Message-----
From: Aleksandra Skoric
Sent: Monday, July 18, 2016 3:21 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Regarding Parameter file not saved
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
>
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Received on Mon Jul 18 2016 - 12:00:02 PDT
