In the last step it gave me following error
> saveamberparm peptide pepide.prmtop peptide.inpcrd
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Could not find bond parameter for: N3 - C
Building angle parameters.
Could not find angle parameter: CX - N3 - C
Could not find angle parameter: H - N3 - C
Could not find angle parameter: H - N3 - C
Could not find angle parameter: H - N3 - C
Could not find angle parameter: N3 - C - CX
Could not find angle parameter: N3 - C - O2
Could not find angle parameter: N3 - C - O2
Building proper torsion parameters.
** No torsion terms for CX-N3-C-CX
** No torsion terms for CX-N3-C-O2
** No torsion terms for CX-N3-C-O2
** No torsion terms for H-N3-C-CX
** No torsion terms for H-N3-C-O2
** No torsion terms for H-N3-C-O2
** No torsion terms for H-N3-C-CX
** No torsion terms for H-N3-C-O2
** No torsion terms for H-N3-C-O2
** No torsion terms for H-N3-C-CX
** No torsion terms for H-N3-C-O2
** No torsion terms for H-N3-C-O2
Building improper torsion parameters.
total 34 improper torsions applied
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.
Parameter file was not saved.
So I was thinking do I need to make frcmod file for this peptide?
But antechamber is not working for this peptide, as it works only for small ligands.
More over if I try to make mol2 file by some software it does not read the frcmod it.
I tell me
Unknown keyword: C.3-C.3-S. in parameter file. Perhaps a format error?
So now I don't know how to tackel this problem
________________________________
From: Carlos Simmerling <carlos.simmerling.gmail.com>
Sent: Thursday, October 20, 2016 4:11:05 AM
To: AMBER Mailing List
Subject: Re: [AMBER] frcmod file error
that looks ok (except the gaff part, it does not look necessary).
what happened when you used this?
On Thu, Oct 20, 2016 at 11:04 AM, Thakur, Abhishek <axt651.miami.edu> wrote:
> Sorry Dr.carlos,
>
> I have a written tutorial, So I have copy pasted it. Just to show how I
> have proceeded
>
>
>
> > tleap -s -f leaprc.ff14SB
>
> > source leaprc.gaff
>
> >peptide = loadpdb 2.pdb
>
> > solvate peptide TIP3PBOX 10>
>
> >charge peptide
>
> > addIons peptide Na+ 2
>
> > loadAmberParams frcmod.ionsjc_tip3p
>
> > saveamberparm peptide peptide.prmtop peptide.inpcrd
>
>
>
> This is what I have done,
>
> ________________________________
> From: Carlos Simmerling <carlos.simmerling.gmail.com>
> Sent: Thursday, October 20, 2016 3:54:36 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] frcmod file error
>
> I find the things you are saying to be confusing. You sent a pdb file
> (2.pdb) that has only normal amino acids and should work fine, but then in
> your email you don't show that this is the pdb file that you used for Leap.
> Also this is just a peptide, so why would you save the files as "complex"?
>
> What error do you get if you try to use only the pdb file that you sent? If
> no error, then what is the pdb file that gives you the error? I still don't
> see anything in what you sent that explains why you are trying to use gaff.
>
> On Thu, Oct 20, 2016 at 10:46 AM, Thakur, Abhishek <axt651.miami.edu>
> wrote:
>
> > yes I have tried that
> >
> >
> > What I did was
> >
> > > > source leaprc.gaff
> > > > loadamberparams PLX4720.frcmod
> > > > solvateBox complex TIP3PBOX 10
> > > > charge complex
> > > > addIons complex Cl- 7
> > > > saveamberparm complex V600E_4720.prmtop V600E_4720.inpcrd
> >
> >
> > and it gave me following error
> >
> > For your reference I have attached my pdb file
> >
> >
> > That is why I was trying to make frcmod file as it is asking me those
> > parameters
> >
> >
> > ________________________________
> > From: Carlos Simmerling <carlos.simmerling.gmail.com>
> > Sent: Thursday, October 20, 2016 3:40:39 AM
> > To: AMBER Mailing List
> > Subject: Re: [AMBER] frcmod file error
> >
> > if it is standard amino acids, I'm not sure I understand why you are
> using
> > a frcmod file.. Did you try without it?
> >
> > On Thu, Oct 20, 2016 at 10:37 AM, Thakur, Abhishek <axt651.miami.edu>
> > wrote:
> >
> > > Hey Dr.David,
> > >
> > >
> > > Thank you for your suggestion, I think I have a cyclic peptide of
> around
> > > 75 atoms, so I think that is why antechamber is not working.
> > >
> > >
> > > So I tried making it as protein is prepared. As I just want to simulate
> > > this peptide by solvating it, so I have not frcmod, lib files of
> > heteroatom
> > > to load.
> > >
> > > So as these are peptide amber should build it as a protein? No hetero
> > atom
> > > only small chain of 9 amino acid in cyclic form.
> > >
> > >
> > > > source leaprc.gaff
> > > > loadamberparams PLX4720.frcmod
> > > > solvateBox complex TIP3PBOX 10
> > > > charge complex
> > > > addIons complex Cl- 7
> > > > saveamberparm complex V600E_4720.prmtop V600E_4720.inpcrd
> > >
> > >
> > > The error that I am getting is
> > >
> > >
> > > Could not find bond parameter for: N3 - C
> > > Building angle parameters.
> > > Could not find angle parameter: CX - N3 - C
> > > Could not find angle parameter: H - N3 - C
> > > Could not find angle parameter: H - N3 - C
> > > Could not find angle parameter: H - N3 - C
> > > Could not find angle parameter: N3 - C - CX
> > > Could not find angle parameter: N3 - C - O2
> > > Could not find angle parameter: N3 - C - O2
> > > Building proper torsion parameters.
> > > ** No torsion terms for CX-N3-C-CX
> > > ** No torsion terms for CX-N3-C-O2
> > > ** No torsion terms for CX-N3-C-O2
> > > ** No torsion terms for H-N3-C-CX
> > > ** No torsion terms for H-N3-C-O2
> > > ** No torsion terms for H-N3-C-O2
> > > ** No torsion terms for H-N3-C-CX
> > > ** No torsion terms for H-N3-C-O2
> > > ** No torsion terms for H-N3-C-O2
> > > ** No torsion terms for H-N3-C-CX
> > > ** No torsion terms for H-N3-C-O2
> > > ** No torsion terms for H-N3-C-O2
> > >
> > >
> > > As antechamber doe not work so I am unable to generate frcmod file
> > > containing this files.
> > >
> > > But as these are just amino acid do I need to give frcmod file or lib
> for
> > > these things?
> > >
> > > If yes then how do I generate it as antechamber is not creating a mol2
> > > file for my peptide and amber gives error if I use mol2 file generated
> by
> > > some other software and make frcmod file.
> > >
> > > Unknown keyword: C.3-C.3-S. in parameter file. Perhaps a format error?
> > >
> > >
> > >
> > > Thanking you,
> > >
> > > Abhsihek
> > >
> > >
> > > ________________________________
> > > From: David A Case <david.case.rutgers.edu>
> > > Sent: Wednesday, October 19, 2016 1:06:36 PM
> > > To: AMBER Mailing List
> > > Subject: Re: [AMBER] frcmod file error
> > >
> > > On Wed, Oct 19, 2016, Thakur, Abhishek wrote:
> > > >
> > > > > antechamber -i PLX4720.pdb -fi pdb -o PLX4720.mol2 -fo mol2 -c bcc
> > -s 2
> > > > But It was continuously giving me error
> > >
> > > > ---Judge bond type for Residue 1 with ID of 1 and Name of GLU ---
> > > >
> > > > ---Judge bond type for Residue 2 with ID of 2 and Name of ASN ---
> > > >
> > > > Warning: the assigned bond types may be wrong, please :
> > > > (1) double check the structure (the connectivity) and/or
> > > > (2) adjust atom valence penalty parameters in APS.DAT, and/or
> > > > (3) increase PSCUTOFF in define.h and recompile bondtype.c
> > > > Be cautious, use a large value of PSCUTOFF (>100) will
> > significantly
> > > increase the computation time
> > >
> > > Note: antechamber is intended for *small molecules*, not for
> polypeptides
> > > or
> > > proteins. Amber builds proteins in a completely different way: please
> > see
> > > the
> > > manual or tutorials.
> > >
> > > [Scott: does acdoctor properly complain if a user tries to use a
> protein
> > > pdb
> > > file?]
> > >
> > > ...good luck...dac
> > >
> > >
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Received on Thu Oct 20 2016 - 08:30:04 PDT
