Re: [AMBER] PMEMD does not support intermolecular PRFs

From: David A Case <>
Date: Thu, 16 Jun 2011 10:13:32 -0400

On Thu, Jun 16, 2011, Maura Catherine Mooney wrote:
> I have little/no experience reading topology files, but I had a look,
> based on your response. Strange behaviour indeed, as there is only
> *intended* to be one GDP molecule, one Mg and 4 coordinating H2O's.

You need to review how you created the topology file in the first place.
I recommend creating a single PDB file with exactly what you want in
it. Change any H2O or HOH labels to WAT; put a TER card between separate
molecules. Remove CONECT records (but be sure to issue a "bond" command
later to leap for any disulfide bonds or other non-standard bonds.) It is
best to put all the water molecules at the end. If there are alternate
conformations in file, choose the one(s) you want and remove the rest.

[In general, careful editing of the input pdb file is required for all but the
simplest protein or nucleic acid systems, and a careful review of what you are
loading is always desirable.]

Then load your force field and any libraries needed for the GDP or Mg
moieties. Issue a single loadpdb command to create the basic system,
follow this by bond, solvateBox and addIons, etc. as appropriate. Then
examine the prmtop file that is created to make sure you have the residues
and ions you want.

...good luck.....dac

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Received on Thu Jun 16 2011 - 07:30:02 PDT
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