AMBER Archive (2008)

Subject: RE: AMBER: initial command?

From: Steve Spronk (spronk_at_umich.edu)
Date: Wed Feb 27 2008 - 12:45:43 CST

As an alternative to doing the bond command in leap, you could write CONECT
records at the oxyt.pdb file specifying the disulfide bond. I know that the
manual (at least for Amber 8, my version) says that CONECT records are
ignored, but the manual is not correct, in my experience.

Either way is fine. CONECT lines in the PDB file or bond commands in leap
are completely equivalent.

-----Original Message-----
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Carlos Simmerling
Sent: Wednesday, February 27, 2008 7:10 AM
To: amber_at_scripps.edu
Subject: Re: AMBER: initial command?

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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