Re: [AMBER] PMEMD does not support intermolecular PRFs

From: Jason Swails <>
Date: Thu, 16 Jun 2011 08:34:17 -0600

I'll add on a little to what Dave said (his advice will help you build a
proper topology):

pmemd expects contiguous molecules. That is, no residue that is *unbonded*
to all of the residues that come before it can come in the middle of some
other molecule. Thus, if a GDP residue is bonded to the rest of a protein
but your MG is not, then your MG should come *after* that GDP.

Leap *should* recognize this and reorder it for you, but I don't know how
much I'd trust either version to do that. When I looked at your topology
file, though, I saw no bonds between your GDP and protein, so heed what Dave
said regarding "bond" commands.

Editing a topology file by hand if you have a lot of experience and
knowledge of the file format is risky. To do it with little
knowledge/experience is an almost guaranteed disaster (relative to what can
go wrong running Amber). I can guarantee you that just removing
RESIDUE_LABELs will kill your topology file (although maybe not with any
discernible error message). You really should recreate your prmtop from
scratch via Dave's advice.


On Thu, Jun 16, 2011 at 8:13 AM, David A Case <>wrote:

> 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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> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER mailing list
Received on Thu Jun 16 2011 - 08:00:03 PDT
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