AMBER Archive (2006)

Subject: Re: AMBER: NAD parameters

From: ivan_at_mmb.pcb.ub.es
Date: Mon Jan 30 2006 - 10:20:19 CST

dear alexandra,

you need to define hibridization for your new atom types using
addatomtypes command of leap, otherwise leap assignes sp0 and gets crazy
when looking for dihedral parameters

something like should be added for each new atom type:

addAtomTypes { { "C1" "C" "sp2" } }

in any case you have parameters for NAD in the contributed parameters
section of the amber web page

http://pharmacy.man.ac.uk/amber/

all the best,

Ivan.

On Mon, 30 Jan 2006 alexandra.marques_at_fc.up.pt wrote:

> Dear Amber users,
>
> I used the parameters files for NAD+ available at
> http://pharmacy.man.ac.uk/amber/ (those produced by Walker et al.). However
> when I load them in xleap together with the pdb file that I am interested a
> weird message appears in the terminal:
>
> -I: Adding /scratch/programs/amber8//dat/leap/prep to search path.
> -I: Adding /scratch/programs/amber8//dat/leap/lib to search path.
> -I: Adding /scratch/programs/amber8//dat/leap/parm to search path.
> -I: Adding /scratch/programs/amber8//dat/leap/cmd to search path.
> -s: Ignoring startup file: leaprc
> -f: Source leaprc.ff99.
> +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
> +---Tried to superimpose torsions for: *-C18-N7-*
> +--- With Sp2 - Sp0
> +--- Sp0 probably means a new atom type is involved
> +--- which needs to be added via addAtomTypes
> +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
> +---Tried to superimpose torsions for: *-C21-N6-*
> +--- With Sp2 - Sp0
> +--- Sp0 probably means a new atom type is involved
> +--- which needs to be added via addAtomTypes
> +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
> +---Tried to superimpose torsions for: *-C16-N6-*
> +--- With Sp2 - Sp0
> +--- Sp0 probably means a new atom type is involved
> +--- which needs to be added via addAtomTypes
> +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
> +---Tried to superimpose torsions for: *-C15-N6-*
> +--- With Sp3 - Sp0
> +--- Sp0 probably means a new atom type is involved
> +--- which needs to be added via addAtomTypes
>
> The commands I used in xleap are:
>
> mods = loadamberparams nad.frcmod
> loadoff nad.off
> x = loadpdb protein.pdb
>
> and the message above appears precisely after I load the pdb file
> containing the
> protein.
> Could someone help me please me? Does anyone know if there is newer parameter
> files for NAD+?
>
>
> Best regards
> Alexandra
>
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-- 
   _______________________________________________
 /                                                 \
/   Ivan Marchan Carvajal                           \
|   (PhD Student)                                   |
|                                                   |
|   Institut de Recerca Biomedica de Barcelona      |
|   Parc Cientific de Barcelona                     |
|   Molecular Modelling & Bionformatics Group       |
|   http://mmb.pcb.ub.es                            |
|                                                   |
|   C/ Josep Samitier 1-5    08028 Barcelona	    |
|   Tel: +34.93.403.71.55   Fax: +34.93.403.71.57   |
|                                                   |
|   E-mail:  ivan_at_mmb.pcb.ub.es                     |
|            theochem_at_hotmail.com                   |
|   Website: http://mmb.pcb.ub.es/~ivan             |
\                                                   /
 \_________________________________________________/

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