AMBER Archive (2004)

Subject: Re: AMBER: AMBER7 plastocyanin tutorial problem.

From: Rhonda Torres (torres_at_scripps.edu)
Date: Fri Aug 06 2004 - 12:57:42 CDT

Hi Tarek,

The output mentions that you are using an atom type what has not been
defined (SD). You would need to add that atom type as suggested:

> Loading PDB file: ./1PLC_nowat_h.pdb
> +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
> +---Tried to superimpose torsions for: *-CE-SD-*
> +--- With Sp3 - Sp0
> +--- Sp0 probably means a new atom type is involved
> +--- which needs to be added via addAtomTypes

We would need to know what you would like to do with that single ZN atom
in order to be of help here. Is it in solution or is it coordinated to
protein residues, etc. Ken Merz Jr. has performed simulations using ZN
coordinated to His, Cys and Asp ligands using Amber (on
metallo-beta-lactamases). You could check those papers for parameters as
a start.

Rhonda

On Fri, 6 Aug 2004, tarek mahfouz wrote:

>
> Hi all,
>
> I'm a new user of AMBER and I'm trying to run the plastocyanin tutorial and here is what I did:
>
> 1- I prepared the required input files hicu.in and mem.in. However, since later on in the leap.in input file the call is for mem.lib and hicu.lib, I saved hicu.in as hicu.lib and mem.in as mem.lib. They were read ok.
>
> 2- I edited the pdb file as explained and run protonate with no complains. The problem comes when I read in the pdb file I get the following messages:
>
>
>
> > PARM94 = loadamberparams frcmod.pcy
> Loading parameters: ./frcmod.pcy
> Reading force field mod type file (frcmod)
> > plc = loadpdb 1PLC_nowat_h.pdb
> Loading PDB file: ./1PLC_nowat_h.pdb
> +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
> +---Tried to superimpose torsions for: *-CE-SD-*
> +--- With Sp3 - 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: *-CG-SD-*
> +--- With Sp3 - 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: *-CG-SD-*
> +--- With Sp3 - 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: *-CE-SD-*
> +--- With Sp3 - 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: *-CG-SD-*
> +--- With Sp3 - 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: *-CG-SD-*
> +--- With Sp3 - 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: *-CG-SD-*
> +--- With Sp3 - 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: *-CE-SD-*
> +--- With Sp3 - Sp0
> +--- Sp0 probably means a new atom type is involved
> +--- which needs to be added via addAtomTypes
> total atoms in file: 1443
>
>
> Now I do not know whats wrong here? Is it the problem with SD? and how to fix this?
>
>
>
> Also, when I save the prmtop and prmcrd files I get the following message:
>
> Building topology.
> Building atom parameters.
> Building bond parameters.
> Building angle parameters.
> Building proper torsion parameters.
> Building improper torsion parameters.
> old PREP-specified impropers:
> <HIC 37>: -M CA N H
> <HIC 37>: CA +M C O
> <HIC 37>: CE1 CD2 NE2 HE2
> <HIC 37>: CG NE2 CD2 HD2
> <HIC 37>: ND1 NE2 CE1 HE1
> <HIC 37>: ND1 CD2 CG CB
> <MEM 92>: -M CA N H
> <MEM 92>: CA +M C O
> total 288 improper torsions applied
> 8 improper torsions in old prep form
> Building H-Bond parameters.
> Marking per-residue atom chain types.
> (Residues lacking connect0/connect1 -
> these don't have chain types marked:
>
> res total affected
>
> CASN 1
> NILE 1
> )
> (no restraints)
> and I'm concerned about the statement "residue lacking connect0/connect1" does it mean it will not save the N and C termini as charged?
>
> One more question please, I have a ZN atom in a different pdb file, how to get parameters for this ZN?
>
> Thanks for your help.
>
> Tarek
>
>
>
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