Hi,
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 5:17 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Regarding Parameter file not saved
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
_______________________________________________
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http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
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Received on Mon Jul 18 2016 - 14:30:03 PDT
