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 - 08:00:02 PDT
