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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- chemical/x-pdb attachment: 2.pdb
Received on Thu Oct 20 2016 - 08:00:04 PDT
