AMBER Archive (2008)

Subject: Re: AMBER: initial command?

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Wed Feb 27 2008 - 06:10:01 CST

you should probably try changing the CYS in your disulfide to CYX.
also make sure to add the bond in leap. do a search in the archives for
disulfide for more details.

On Wed, Feb 27, 2008 at 7:01 AM, Anamika Awasthi <aawasthi28_at_gmail.com> wrote:
> my first command is showing this -----> why?
> tleap -s -f oxy.scr
> -I: Adding /usr/local/Amber9/amber9//dat/leap/prep to search path.
> -I: Adding /usr/local/Amber9/amber9//dat/leap/lib to search path.
> -I: Adding /usr/local/Amber9/amber9//dat/leap/parm to search path.
> -I: Adding /usr/local/Amber9/amber9//dat/leap/cmd to search path.
> -s: Ignoring startup file: leaprc
> -f: Source oxy.scr.
>
> Welcome to LEaP!
> Sourcing: ./oxy.scr
> ----- Source: /usr/local/Amber9/amber9//dat/leap/cmd/leaprc.ff03
> ----- Source of /usr/local/Amber9/amber9//dat/leap/cmd/leaprc.ff03 done
> Log file: ./leap.log
> Loading parameters: /usr/local/Amber9/amber9//dat/leap/parm/parm99.dat
> Reading title:
> PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP
> incl.02/04/99
> Loading parameters: /usr/local/Amber9/amber9//dat/leap/parm/frcmod.ff03
> Reading force field modification type file (frcmod)
> Reading title:
> Duan et al ff03 phi psi torsions
> Loading library: /usr/local/Amber9/amber9//dat/leap/lib/ions94.lib
> Loading library: /usr/local/Amber9/amber9//dat/leap/lib/solvents.lib
> Loading library: /usr/local/Amber9/amber9//dat/leap/lib/all_nucleic94.lib
> Loading library: /usr/local/Amber9/amber9//dat/leap/lib/all_aminoct94.lib
> Loading library: /usr/local/Amber9/amber9//dat/leap/lib/all_aminont94.lib
> Loading library: /usr/local/Amber9/amber9//dat/leap/lib/all_amino03.lib
> Loading parameters: /usr/local/Amber9/amber9//dat/leap/parm/frcmod.spce
> Reading force field modification type file (frcmod)
> Reading title:
> This is the additional/replacement parameter set for SPC/E water
> Loading PDB file: ./oxyt.pdb
> Added missing heavy atom: .R<CGLY 9>.A<OXT 8>
> total atoms in file: 68
> Leap added 68 missing atoms according to residue templates:
> 1 Heavy
> 67 H / lone pairs
> Checking 'oxy'....
> Warning: Close contact of 1.831870 angstroms between .R<ASN 5>.A<H 2> and
> .R<CYS 6>.A<H 2>
> Checking parameters for unit 'oxy'.
> Checking for bond parameters.
> Could not find bond parameter for: SH - SH
> Could not find bond parameter for: SH - SH
> Checking for angle parameters.
> Could not find angle parameter: HS - SH - SH
> Could not find angle parameter: HS - SH - SH
> Could not find angle parameter: SH - SH - CT
> Could not find angle parameter: SH - SH - HS
> Could not find angle parameter: SH - SH - CT
> Could not find angle parameter: SH - SH - HS
> Could not find angle parameter: CT - SH - SH
> Could not find angle parameter: CT - SH - SH
> There are missing parameters.
> check: Warnings: 1
> Unit is OK.
> Checking Unit.
> Building topology.
> Building atom parameters.
> Building bond parameters.
> Could not find bond parameter for: SH - SH
> Could not find bond parameter for: SH - SH
> Building angle parameters.
> Could not find angle parameter: HS - SH - SH
> Could not find angle parameter: HS - SH - SH
> Could not find angle parameter: SH - SH - CT
> Could not find angle parameter: SH - SH - HS
> Could not find angle parameter: SH - SH - CT
> Could not find angle parameter: SH - SH - HS
> Could not find angle parameter: CT - SH - SH
> Could not find angle parameter: CT - SH - SH
> Building proper torsion parameters.
> !FATAL ERROR----------------------------------------
> !FATAL: In file [unitio.c], line 1769
> !FATAL: Message: 1-4: cannot add bond 10 92
> !
> !ABORTING.
>
>
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