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.
Just in case that You stuck in procedures I can help You with files:
*.prmtop, *.inpcrd, *.pdb - solvated too -, pdb mol2 ...etc (commands list
as well), important for your case. However, before u ask for it I really
advice to do the example from tutorial page:
http://ambermd.org/tutorials/basic/tutorial4b/index.htm, and then let me
know if you meet a problem .
Cheers
Zoran
-----Original Message-----
From: Vishal Nemaysh
Sent: Monday, July 18, 2016 11:31 AM
To: AMBER Mailing List
Subject: Re: [AMBER] Regarding Parameter file not saved
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.
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
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Received on Tue Jul 19 2016 - 01:30:02 PDT
