Hi,
On Fri, 30 Jan 2009, balaji nagarajan wrote:
> I have tried to generate prmtop and inpcrd files using
> a PDB which has MG2 .
> ------------------------------------------------------------------------------
> Loading PDB file: ./mg_dec2.pdb
> Created a new atom named: MG2 within residue: .R<MG2 41>
> Added missing heavy atom: .R<MG2 41>.A<MG 1>
...
> total atoms in file: 812
> Leap added 456 missing atoms according to residue templates:
> 4 Heavy
> 452 H / lone pairs
> The file contained 4 atoms not in residue templates
> ---------------------------------------------------------------------------------------------
> saveamberparmtop command
> the MG2 error came as
> ----------------------------------------------------------------------------------------------
> FATAL: Atom .R<MG2 41>.A<MG2 2> does not have a type.
...
> Failed to generate parameters
> Parameter file was not saved.
>
> ---------------------------------------------------------------------------------------------
Did you load the appropriate ions library ? E.g.
loadoff ions94.lib
See these for many more details:
http://archive.ambermd.org/200807/0142.html
http://archive.ambermd.org/200807/0433.html
Scott
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Received on Wed Feb 04 2009 - 01:33:02 PST
